From 699c1abc8728a4d145445aaaca215010866d1b23 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Thu, 29 Aug 2024 17:02:00 +0100
Subject: [PATCH 01/33] Used the same kwargs method as in the CNV function

---
 malariagen_data/anoph/g123.py | 18 ++++++++++++++----
 malariagen_data/anoph/h12.py  | 18 ++++++++++++++----
 malariagen_data/anoph/h1x.py  | 18 ++++++++++++++----
 3 files changed, 42 insertions(+), 12 deletions(-)

diff --git a/malariagen_data/anoph/g123.py b/malariagen_data/anoph/g123.py
index 0e6da1ea2..639058021 100644
--- a/malariagen_data/anoph/g123.py
+++ b/malariagen_data/anoph/g123.py
@@ -319,6 +319,7 @@ def plot_g123_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
+        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -375,15 +376,22 @@ def plot_g123_gwss_track(
             output_backend=output_backend,
         )
 
+        circle_kwargs_mutable = dict(circle_kwargs) if circle_kwargs else {}
+        circle_kwargs_mutable["size"] = circle_kwargs_mutable.get("size", 3)
+        circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get("line_width", 1)
+        circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
+            "line_color", "black"
+        )
+        circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
+            "fill_color", None
+        )
+
         # plot G123
         fig.scatter(
             x=x,
             y=g123,
-            size=3,
             marker="circle",
-            line_width=1,
-            line_color="black",
-            fill_color=None,
+            **circle_kwargs_mutable,
         )
 
         # tidy up the plot
@@ -420,6 +428,7 @@ def plot_g123_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 170,
+        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -441,6 +450,7 @@ def plot_g123_gwss(
             sizing_mode=sizing_mode,
             width=width,
             height=track_height,
+            circle_kwargs=circle_kwargs,
             show=False,
             output_backend=output_backend,
             inline_array=inline_array,
diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index e01510b8b..91f5b7484 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -325,6 +325,7 @@ def plot_h12_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
+        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -377,15 +378,22 @@ def plot_h12_gwss_track(
             output_backend=output_backend,
         )
 
+        circle_kwargs_mutable = dict(circle_kwargs) if circle_kwargs else {}
+        circle_kwargs_mutable["size"] = circle_kwargs_mutable.get("size", 3)
+        circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get("line_width", 1)
+        circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
+            "line_color", "black"
+        )
+        circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
+            "fill_color", None
+        )
+
         # Plot H12.
         fig.scatter(
             x=x,
             y=h12,
             marker="circle",
-            size=3,
-            line_width=1,
-            line_color="black",
-            fill_color=None,
+            **circle_kwargs_mutable,
         )
 
         # Tidy up the plot.
@@ -422,6 +430,7 @@ def plot_h12_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 170,
+        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -441,6 +450,7 @@ def plot_h12_gwss(
             sizing_mode=sizing_mode,
             width=width,
             height=track_height,
+            circle_kwargs=circle_kwargs,
             show=False,
             output_backend=output_backend,
         )
diff --git a/malariagen_data/anoph/h1x.py b/malariagen_data/anoph/h1x.py
index 732a07636..22ba797ea 100644
--- a/malariagen_data/anoph/h1x.py
+++ b/malariagen_data/anoph/h1x.py
@@ -166,6 +166,7 @@ def plot_h1x_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
+        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -219,15 +220,22 @@ def plot_h1x_gwss_track(
             output_backend=output_backend,
         )
 
+        circle_kwargs_mutable = dict(circle_kwargs) if circle_kwargs else {}
+        circle_kwargs_mutable["size"] = circle_kwargs_mutable.get("size", 3)
+        circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get("line_width", 1)
+        circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
+            "line_color", "black"
+        )
+        circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
+            "fill_color", None
+        )
+
         # Plot H1X.
         fig.scatter(
             x=x,
             y=h1x,
             marker="circle",
-            size=3,
-            line_width=1,
-            line_color="black",
-            fill_color=None,
+            **circle_kwargs_mutable,
         )
 
         # Tidy up the plot.
@@ -268,6 +276,7 @@ def plot_h1x_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 190,
+        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -288,6 +297,7 @@ def plot_h1x_gwss(
             sizing_mode=sizing_mode,
             width=width,
             height=track_height,
+            circle_kwargs=circle_kwargs,
             show=False,
             output_backend=output_backend,
         )

From e7e6b71ab1bba414bfef5255ddcef62a61ad36a9 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 30 Sep 2024 16:19:18 +0100
Subject: [PATCH 02/33] Color depending on contig. Still imperfect.

---
 malariagen_data/anoph/h12.py | 113 +++++++++++++++++++++++++++++++++--
 1 file changed, 107 insertions(+), 6 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 91f5b7484..1a0694d6a 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -208,7 +208,7 @@ def plot_h12_calibration(
         else:
             return fig
 
-    def _h12_gwss(
+    def _h12_gwss_contig(
         self,
         contig,
         analysis,
@@ -242,11 +242,97 @@ def _h12_gwss(
             # Compute window midpoints.
             pos = ds_haps["variant_position"].values
             x = allel.moving_statistic(pos, statistic=np.mean, size=window_size)
+            contigs = allel.moving_statistic(
+                ds_haps["variant_contig"].values, statistic=np.median, size=window_size
+            )
 
-        results = dict(x=x, h12=h12)
+        results = dict(x=x, h12=h12, contigs=contigs)
 
         return results
 
+    def _h12_gwss(
+        self,
+        contig,
+        analysis,
+        window_size,
+        sample_sets,
+        sample_query,
+        cohort_size,
+        min_cohort_size,
+        max_cohort_size,
+        random_seed,
+    ):
+        results_tmp = self._h12_gwss_contig(
+            contig=contig,
+            analysis=analysis,
+            window_size=window_size,
+            sample_query=sample_query,
+            sample_sets=sample_sets,
+            cohort_size=cohort_size,
+            min_cohort_size=min_cohort_size,
+            max_cohort_size=max_cohort_size,
+            random_seed=random_seed,
+        )
+        results = dict(x=results_tmp["x"], h12=results_tmp["h12"])
+
+        return results
+
+    @check_types
+    @doc(
+        summary="Run h12 genome-wide selection scan.",
+        returns=dict(
+            x="An array containing the window centre point genomic positions.",
+            h12="An array with h12 statistic values for each window.",
+        ),
+    )
+    def h12_gwss_contig(
+        self,
+        contig: base_params.contig,
+        window_size: h12_params.window_size,
+        analysis: hap_params.analysis = base_params.DEFAULT,
+        sample_query: Optional[base_params.sample_query] = None,
+        sample_sets: Optional[base_params.sample_sets] = None,
+        cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default,
+        min_cohort_size: Optional[
+            base_params.min_cohort_size
+        ] = h12_params.min_cohort_size_default,
+        max_cohort_size: Optional[
+            base_params.max_cohort_size
+        ] = h12_params.max_cohort_size_default,
+        random_seed: base_params.random_seed = 42,
+    ) -> Tuple[np.ndarray, np.ndarray]:
+        # Change this name if you ever change the behaviour of this function, to
+        # invalidate any previously cached data.
+        name = "h12_gwss_v1"
+
+        params = dict(
+            contig=contig,
+            analysis=self._prep_phasing_analysis_param(analysis=analysis),
+            window_size=window_size,
+            sample_sets=self._prep_sample_sets_param(sample_sets=sample_sets),
+            # N.B., do not be tempted to convert this sample query into integer
+            # indices using _prep_sample_selection_params, because the indices
+            # are different in the haplotype data.
+            sample_query=sample_query,
+            cohort_size=cohort_size,
+            min_cohort_size=min_cohort_size,
+            max_cohort_size=max_cohort_size,
+            random_seed=random_seed,
+        )
+
+        #        try:
+        #            results = self.results_cache_get(name=name, params=params)
+
+        #        except CacheMiss:
+        results = self._h12_gwss_contig(**params)
+        self.results_cache_set(name=name, params=params, results=results)
+
+        x = results["x"]
+        h12 = results["h12"]
+        contigs = results["contigs"]
+
+        return x, h12, contigs
+
     @check_types
     @doc(
         summary="Run h12 genome-wide selection scan.",
@@ -331,7 +417,7 @@ def plot_h12_gwss_track(
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
     ) -> gplt_params.figure:
         # Compute H12.
-        x, h12 = self.h12_gwss(
+        x, h12, contigs = self.h12_gwss_contig(
             contig=contig,
             analysis=analysis,
             window_size=window_size,
@@ -343,6 +429,9 @@ def plot_h12_gwss_track(
             random_seed=random_seed,
         )
 
+        # Hard coded contig colors: not good
+        color_dict = {0: "red", 1: "blue", 2: "orange", 3: "green", 4: "purple"}
+
         # Determine X axis range.
         x_min = x[0]
         x_max = x[-1]
@@ -381,9 +470,9 @@ def plot_h12_gwss_track(
         circle_kwargs_mutable = dict(circle_kwargs) if circle_kwargs else {}
         circle_kwargs_mutable["size"] = circle_kwargs_mutable.get("size", 3)
         circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get("line_width", 1)
-        circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
-            "line_color", "black"
-        )
+        # circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
+        #    "line_color", "black"
+        # )
         circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
             "fill_color", None
         )
@@ -396,6 +485,18 @@ def plot_h12_gwss_track(
             **circle_kwargs_mutable,
         )
 
+        # Plot H12.
+        for s in set(contigs):
+            color = color_dict[s]
+            idxs = contigs == s
+            fig.scatter(
+                x=x[idxs],
+                y=h12[idxs],
+                marker="circle",
+                line_color=color,
+                **circle_kwargs_mutable,
+            )
+
         # Tidy up the plot.
         fig.yaxis.axis_label = "H12"
         fig.yaxis.ticker = [0, 1]

From 787045a2bbfdfe7b6f29f5b71a6105fb170d2902 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 30 Sep 2024 16:23:12 +0100
Subject: [PATCH 03/33] Corrected wrong type.

---
 malariagen_data/anoph/h12.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 1a0694d6a..47379730e 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -300,7 +300,7 @@ def h12_gwss_contig(
             base_params.max_cohort_size
         ] = h12_params.max_cohort_size_default,
         random_seed: base_params.random_seed = 42,
-    ) -> Tuple[np.ndarray, np.ndarray]:
+    ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
         # Change this name if you ever change the behaviour of this function, to
         # invalidate any previously cached data.
         name = "h12_gwss_v1"

From 2ae87be0fa0db12927b1af3d32e51ceb8c441a23 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 30 Sep 2024 16:27:10 +0100
Subject: [PATCH 04/33] Corrected the doc.

---
 malariagen_data/anoph/h12.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 47379730e..f2e22ec49 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -283,6 +283,7 @@ def _h12_gwss(
         returns=dict(
             x="An array containing the window centre point genomic positions.",
             h12="An array with h12 statistic values for each window.",
+            contigs="An array with the contig for each window. The median is chosen for windows overlapping a change of contig.",
         ),
     )
     def h12_gwss_contig(

From c3834bd2f861eda2198031ed0ff38a7fea5ca6c2 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 30 Sep 2024 16:40:06 +0100
Subject: [PATCH 05/33] Something weird changed the test while they were being
 performed.

---
 malariagen_data/anoph/h12.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 3c85d11c4..ab93d6ced 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -277,6 +277,8 @@ def _h12_gwss(
         min_cohort_size,
         max_cohort_size,
         random_seed,
+        chunks,
+        inline_array,
     ):
         results_tmp = self._h12_gwss_contig(
             contig=contig,
@@ -288,6 +290,8 @@ def _h12_gwss(
             min_cohort_size=min_cohort_size,
             max_cohort_size=max_cohort_size,
             random_seed=random_seed,
+            chunks=chunks,
+            inline_array=inline_array,
         )
         results = dict(x=results_tmp["x"], h12=results_tmp["h12"])
 

From df0a0c5a7aad14e63e38634118cc3c57510f8da5 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 30 Sep 2024 16:52:43 +0100
Subject: [PATCH 06/33] Still a lot of weird stuff.

---
 malariagen_data/anoph/h12.py | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index ab93d6ced..f5f21a971 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -321,6 +321,8 @@ def h12_gwss_contig(
             base_params.max_cohort_size
         ] = h12_params.max_cohort_size_default,
         random_seed: base_params.random_seed = 42,
+        chunks: base_params.chunks = base_params.native_chunks,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
     ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
         # Change this name if you ever change the behaviour of this function, to
         # invalidate any previously cached data.
@@ -339,14 +341,18 @@ def h12_gwss_contig(
             min_cohort_size=min_cohort_size,
             max_cohort_size=max_cohort_size,
             random_seed=random_seed,
+            chunks=chunks,
+            inline_array=inline_array,
         )
 
-        #        try:
-        #            results = self.results_cache_get(name=name, params=params)
+        try:
+            results = self.results_cache_get(name=name, params=params)
 
-        #        except CacheMiss:
-        results = self._h12_gwss_contig(**params)
-        self.results_cache_set(name=name, params=params, results=results)
+        except CacheMiss:
+            results = self._h12_gwss_contig(
+                chunks=chunks, inline_array=inline_array, **params
+            )
+            self.results_cache_set(name=name, params=params, results=results)
 
         x = results["x"]
         h12 = results["h12"]

From 52acfef6aeb367b38aaa5effde328e44dcfa392c Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 30 Sep 2024 17:04:44 +0100
Subject: [PATCH 07/33] Still more weird stuff.

---
 malariagen_data/anoph/h12.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index f5f21a971..c02e89598 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -349,9 +349,7 @@ def h12_gwss_contig(
             results = self.results_cache_get(name=name, params=params)
 
         except CacheMiss:
-            results = self._h12_gwss_contig(
-                chunks=chunks, inline_array=inline_array, **params
-            )
+            results = self._h12_gwss_contig(**params)
             self.results_cache_set(name=name, params=params, results=results)
 
         x = results["x"]

From 212b164aad96a35dd39c91c9d1dbfc442a8fd2b2 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 30 Sep 2024 17:07:18 +0100
Subject: [PATCH 08/33] Even more weird stuff.

---
 malariagen_data/anoph/h12.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index c02e89598..9c9330c9e 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -341,15 +341,15 @@ def h12_gwss_contig(
             min_cohort_size=min_cohort_size,
             max_cohort_size=max_cohort_size,
             random_seed=random_seed,
-            chunks=chunks,
-            inline_array=inline_array,
         )
 
         try:
             results = self.results_cache_get(name=name, params=params)
 
         except CacheMiss:
-            results = self._h12_gwss_contig(**params)
+            results = self._h12_gwss_contig(
+                chunks=chunks, inline_array=inline_array, **params
+            )
             self.results_cache_set(name=name, params=params, results=results)
 
         x = results["x"]

From bda3efee22cb828137767e4fc4cfa07ff311047f Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 30 Sep 2024 18:02:35 +0100
Subject: [PATCH 09/33] The solution was obvious.

---
 malariagen_data/anoph/h12.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 9c9330c9e..19d44a442 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -326,7 +326,7 @@ def h12_gwss_contig(
     ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
         # Change this name if you ever change the behaviour of this function, to
         # invalidate any previously cached data.
-        name = "h12_gwss_v1"
+        name = "h12_gwss_contig_v1"
 
         params = dict(
             contig=contig,

From c63b572c85c2d9170ef72d4ecad032a21db9f9e8 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Tue, 1 Oct 2024 12:11:15 +0100
Subject: [PATCH 10/33] Time for a detour.

---
 malariagen_data/anoph/gplt_params.py | 10 +++++++++-
 malariagen_data/anoph/h12.py         | 27 +++++++--------------------
 2 files changed, 16 insertions(+), 21 deletions(-)

diff --git a/malariagen_data/anoph/gplt_params.py b/malariagen_data/anoph/gplt_params.py
index 6612e981d..c0f521ecc 100644
--- a/malariagen_data/anoph/gplt_params.py
+++ b/malariagen_data/anoph/gplt_params.py
@@ -1,7 +1,7 @@
 """Parameters for genome plotting functions. N.B., genome plots are always
 plotted with bokeh."""
 
-from typing import Literal, Mapping, Optional, Union
+from typing import Literal, Mapping, Optional, Union, Final
 
 import bokeh.models
 from typing_extensions import Annotated, TypeAlias
@@ -103,3 +103,11 @@
     Mapping,
     "Passed through to bokeh line() function.",
 ]
+
+circle_kwargs_dict: Final[dict[int, circle_kwargs]] = {
+    0: {"line_color": "red", "size": 3, "line_width": 1, "fill_color": None},
+    1: {"line_color": "blue", "size": 3, "line_width": 1, "fill_color": None},
+    2: {"line_color": "orange", "size": 3, "line_width": 1, "fill_color": None},
+    3: {"line_color": "green", "size": 3, "line_width": 1, "fill_color": None},
+    4: {"line_color": "purple", "size": 3, "line_width": 1, "fill_color": None},
+}
diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 19d44a442..5a5248d79 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -460,9 +460,6 @@ def plot_h12_gwss_track(
             inline_array=inline_array,
         )
 
-        # Hard coded contig colors: not good
-        color_dict = {0: "red", 1: "blue", 2: "orange", 3: "green", 4: "purple"}
-
         # Determine X axis range.
         x_min = x[0]
         x_max = x[-1]
@@ -498,34 +495,24 @@ def plot_h12_gwss_track(
             output_backend=output_backend,
         )
 
-        circle_kwargs_mutable = dict(circle_kwargs) if circle_kwargs else {}
-        circle_kwargs_mutable["size"] = circle_kwargs_mutable.get("size", 3)
-        circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get("line_width", 1)
+        # circle_kwargs_mutable = dict(circle_kwargs) if circle_kwargs else {}
+        # circle_kwargs_mutable["size"] = circle_kwargs_mutable.get("size", 3)
+        # circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get("line_width", 1)
         # circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
         #    "line_color", "black"
         # )
-        circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
-            "fill_color", None
-        )
-
-        # Plot H12.
-        fig.scatter(
-            x=x,
-            y=h12,
-            marker="circle",
-            **circle_kwargs_mutable,
-        )
+        # circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
+        #    "fill_color", None
+        # )
 
         # Plot H12.
         for s in set(contigs):
-            color = color_dict[s]
             idxs = contigs == s
             fig.scatter(
                 x=x[idxs],
                 y=h12[idxs],
                 marker="circle",
-                line_color=color,
-                **circle_kwargs_mutable,
+                **gplt_params.circle_kwargs_dict[s],
             )
 
         # Tidy up the plot.

From 7fd9c4b60e0ef2fd0a47bb0a0f9c13d4f42abd2a Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Tue, 1 Oct 2024 14:27:07 +0100
Subject: [PATCH 11/33] Uniformised the basic and user-provided option,
 somewhat.

---
 malariagen_data/anoph/h12.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 5a5248d79..2edd92d99 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -508,11 +508,24 @@ def plot_h12_gwss_track(
         # Plot H12.
         for s in set(contigs):
             idxs = contigs == s
+            circle_kwargs_mutable = dict(circle_kwargs[s]) if circle_kwargs else {}
+            circle_kwargs_mutable["size"] = circle_kwargs_mutable.get(
+                "size", gplt_params.circle_kwargs_dict[s]["size"]
+            )
+            circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get(
+                "line_width", gplt_params.circle_kwargs_dict[s]["line_width"]
+            )
+            circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
+                "line_color", gplt_params.circle_kwargs_dict[s]["line_color"]
+            )
+            circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
+                "fill_color", gplt_params.circle_kwargs_dict[s]["fill_color"]
+            )
             fig.scatter(
                 x=x[idxs],
                 y=h12[idxs],
                 marker="circle",
-                **gplt_params.circle_kwargs_dict[s],
+                **circle_kwargs_mutable,
             )
 
         # Tidy up the plot.

From 5a79a11db347e6863d125a380776d65b5ea999ea Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Tue, 1 Oct 2024 14:35:54 +0100
Subject: [PATCH 12/33] A bit of clean-up.

---
 malariagen_data/anoph/h12.py | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 2edd92d99..d0bcee7cc 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -495,16 +495,6 @@ def plot_h12_gwss_track(
             output_backend=output_backend,
         )
 
-        # circle_kwargs_mutable = dict(circle_kwargs) if circle_kwargs else {}
-        # circle_kwargs_mutable["size"] = circle_kwargs_mutable.get("size", 3)
-        # circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get("line_width", 1)
-        # circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
-        #    "line_color", "black"
-        # )
-        # circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
-        #    "fill_color", None
-        # )
-
         # Plot H12.
         for s in set(contigs):
             idxs = contigs == s

From 87e27f2a1a4d4f776772e83811df286bc545bd47 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Tue, 1 Oct 2024 14:49:55 +0100
Subject: [PATCH 13/33] Corrected a wrong type.

---
 malariagen_data/anoph/h12.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index d0bcee7cc..e96ab7a65 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -438,7 +438,7 @@ def plot_h12_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
-        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
+        circle_kwargs_dict: Optional[gplt_params.circle_kwargs_dict] = None,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -498,18 +498,20 @@ def plot_h12_gwss_track(
         # Plot H12.
         for s in set(contigs):
             idxs = contigs == s
-            circle_kwargs_mutable = dict(circle_kwargs[s]) if circle_kwargs else {}
+            circle_kwargs_mutable = (
+                dict(circle_kwargs_dict[s]) if circle_kwargs_dict else {}
+            )
             circle_kwargs_mutable["size"] = circle_kwargs_mutable.get(
-                "size", gplt_params.circle_kwargs_dict[s]["size"]
+                "size", gplt_params.default_circle_kwargs_dict[s]["size"]
             )
             circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get(
-                "line_width", gplt_params.circle_kwargs_dict[s]["line_width"]
+                "line_width", gplt_params.default_circle_kwargs_dict[s]["line_width"]
             )
             circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
-                "line_color", gplt_params.circle_kwargs_dict[s]["line_color"]
+                "line_color", gplt_params.default_circle_kwargs_dict[s]["line_color"]
             )
             circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
-                "fill_color", gplt_params.circle_kwargs_dict[s]["fill_color"]
+                "fill_color", gplt_params.default_circle_kwargs_dict[s]["fill_color"]
             )
             fig.scatter(
                 x=x[idxs],

From 948f86bba4e429126b96fecd721ab81cd979c549 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Tue, 1 Oct 2024 14:56:24 +0100
Subject: [PATCH 14/33] Added the wrong params file.

---
 malariagen_data/anoph/gplt_params.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/malariagen_data/anoph/gplt_params.py b/malariagen_data/anoph/gplt_params.py
index c0f521ecc..90d93ac97 100644
--- a/malariagen_data/anoph/gplt_params.py
+++ b/malariagen_data/anoph/gplt_params.py
@@ -104,7 +104,12 @@
     "Passed through to bokeh line() function.",
 ]
 
-circle_kwargs_dict: Final[dict[int, circle_kwargs]] = {
+circle_kwargs_dict: TypeAlias = Annotated[
+    dict[int, circle_kwargs],
+    "A dictionary of arguments passed through to bokeh scatter() function with marker = 'circle' with a value per contig.",
+]
+
+default_circle_kwargs_dict: Final[dict[int, circle_kwargs]] = {
     0: {"line_color": "red", "size": 3, "line_width": 1, "fill_color": None},
     1: {"line_color": "blue", "size": 3, "line_width": 1, "fill_color": None},
     2: {"line_color": "orange", "size": 3, "line_width": 1, "fill_color": None},

From e49755fe2d9383ca5cf5979b8a84213d7fa10f45 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Tue, 1 Oct 2024 15:06:44 +0100
Subject: [PATCH 15/33] Forgot to forward a change.

---
 malariagen_data/anoph/h12.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index e96ab7a65..2f71f80b5 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -554,7 +554,7 @@ def plot_h12_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 170,
-        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
+        circle_kwargs_dict: Optional[gplt_params.circle_kwargs_dict] = None,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -576,7 +576,7 @@ def plot_h12_gwss(
             sizing_mode=sizing_mode,
             width=width,
             height=track_height,
-            circle_kwargs=circle_kwargs,
+            circle_kwargs_dict=circle_kwargs_dict,
             show=False,
             output_backend=output_backend,
             chunks=chunks,

From 01ad5e34160c778eb1d454eb199ca883479b80db Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Wed, 2 Oct 2024 09:52:30 +0100
Subject: [PATCH 16/33] Updated the tests a bit.

---
 tests/anoph/test_h12.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/tests/anoph/test_h12.py b/tests/anoph/test_h12.py
index d0a2d9980..b516b88eb 100644
--- a/tests/anoph/test_h12.py
+++ b/tests/anoph/test_h12.py
@@ -142,10 +142,22 @@ def check_h12_gwss(*, api, h12_params):
     assert np.all(h12 >= 0)
     assert np.all(h12 <= 1)
 
+    circle_kwargs_dict = {
+        0: {"line_color": "black", "size": 5, "line_width": 1, "fill_color": None},
+        1: {"line_color": "green", "size": 4, "line_width": 2, "fill_color": "black"},
+        2: {"line_color": "orange", "size": 3, "line_width": 1, "fill_color": None},
+        3: {"line_color": "green", "size": 2, "line_width": 2, "fill_color": "black"},
+        4: {"line_color": "purple", "size": 1, "line_width": 1, "fill_color": None},
+    }
+
     # Check plotting functions.
-    fig = api.plot_h12_gwss_track(**h12_params, show=False)
+    fig = api.plot_h12_gwss_track(
+        **h12_params, circle_kwargs_dict=circle_kwargs_dict, show=False
+    )
     assert isinstance(fig, bokeh.models.Plot)
-    fig = api.plot_h12_gwss(**h12_params, show=False)
+    fig = api.plot_h12_gwss(
+        **h12_params, circle_kwargs_dict=circle_kwargs_dict, show=False
+    )
     assert isinstance(fig, bokeh.models.GridPlot)
 
 

From b2d9b0ae572e0b51f0d46ea98b7a7aa14c58ce18 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Wed, 2 Oct 2024 16:31:58 +0100
Subject: [PATCH 17/33] Dealt with h1x.

---
 malariagen_data/anoph/h1x.py | 154 ++++++++++++++++++++++++++++++-----
 tests/anoph/test_h1x.py      |  12 ++-
 2 files changed, 143 insertions(+), 23 deletions(-)

diff --git a/malariagen_data/anoph/h1x.py b/malariagen_data/anoph/h1x.py
index 2f0276853..994728b10 100644
--- a/malariagen_data/anoph/h1x.py
+++ b/malariagen_data/anoph/h1x.py
@@ -24,7 +24,7 @@ def __init__(
         # to the superclass constructor.
         super().__init__(**kwargs)
 
-    def _h1x_gwss(
+    def _h1x_gwss_contig(
         self,
         contig,
         analysis,
@@ -80,11 +80,114 @@ def _h1x_gwss(
             # Compute window midpoints.
             pos = ds1["variant_position"].values
             x = allel.moving_statistic(pos, statistic=np.mean, size=window_size)
+            contigs = allel.moving_statistic(
+                ds1["variant_contig"].values, statistic=np.median, size=window_size
+            )
 
-        results = dict(x=x, h1x=h1x)
+        results = dict(x=x, h1x=h1x, contigs=contigs)
 
         return results
 
+    def _h1x_gwss(
+        self,
+        contig,
+        analysis,
+        window_size,
+        sample_sets,
+        cohort1_query,
+        cohort2_query,
+        cohort_size,
+        min_cohort_size,
+        max_cohort_size,
+        random_seed,
+        chunks,
+        inline_array,
+    ):
+        results_tmp = self._h1x_gwss_contig(
+            contig=contig,
+            analysis=analysis,
+            window_size=window_size,
+            cohort1_query=cohort1_query,
+            cohort2_query=cohort2_query,
+            sample_sets=sample_sets,
+            cohort_size=cohort_size,
+            min_cohort_size=min_cohort_size,
+            max_cohort_size=max_cohort_size,
+            random_seed=random_seed,
+            chunks=chunks,
+            inline_array=inline_array,
+        )
+
+        results = dict(x=results_tmp["x"], h1x=results_tmp["h1x"])
+
+        return results
+
+    @check_types
+    @doc(
+        summary="""
+            Run a H1X genome-wide scan to detect genome regions with
+            shared selective sweeps between two cohorts.
+        """,
+        returns=dict(
+            x="An array containing the window centre point genomic positions.",
+            h1x="An array with H1X statistic values for each window.",
+            contigs="An array with the contig for each window. The median is chosen for windows overlapping a change of contig.",
+        ),
+    )
+    def h1x_gwss_contig(
+        self,
+        contig: base_params.contig,
+        window_size: h12_params.window_size,
+        cohort1_query: base_params.sample_query,
+        cohort2_query: base_params.sample_query,
+        analysis: hap_params.analysis = base_params.DEFAULT,
+        sample_sets: Optional[base_params.sample_sets] = None,
+        cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default,
+        min_cohort_size: Optional[
+            base_params.min_cohort_size
+        ] = h12_params.min_cohort_size_default,
+        max_cohort_size: Optional[
+            base_params.max_cohort_size
+        ] = h12_params.max_cohort_size_default,
+        random_seed: base_params.random_seed = 42,
+        chunks: base_params.chunks = base_params.native_chunks,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
+    ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
+        # Change this name if you ever change the behaviour of this function, to
+        # invalidate any previously cached data.
+        name = "h1x_gwss_contig_v1"
+
+        params = dict(
+            contig=contig,
+            analysis=self._prep_phasing_analysis_param(analysis=analysis),
+            window_size=window_size,
+            # N.B., do not be tempted to convert these sample queries into integer
+            # indices using _prep_sample_selection_params, because the indices
+            # are different in the haplotype data.
+            cohort1_query=cohort1_query,
+            cohort2_query=cohort2_query,
+            sample_sets=self._prep_sample_sets_param(sample_sets=sample_sets),
+            cohort_size=cohort_size,
+            min_cohort_size=min_cohort_size,
+            max_cohort_size=max_cohort_size,
+            random_seed=random_seed,
+        )
+
+        try:
+            results = self.results_cache_get(name=name, params=params)
+
+        except CacheMiss:
+            results = self._h1x_gwss_contig(
+                chunks=chunks, inline_array=inline_array, **params
+            )
+            self.results_cache_set(name=name, params=params, results=results)
+
+        x = results["x"]
+        h1x = results["h1x"]
+        contigs = results["contigs"]
+
+        return x, h1x, contigs
+
     @check_types
     @doc(
         summary="""
@@ -174,7 +277,7 @@ def plot_h1x_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
-        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
+        circle_kwargs_dict: Optional[gplt_params.circle_kwargs_dict] = None,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -182,7 +285,7 @@ def plot_h1x_gwss_track(
         inline_array: base_params.inline_array = base_params.inline_array_default,
     ) -> gplt_params.figure:
         # Compute H1X.
-        x, h1x = self.h1x_gwss(
+        x, h1x, contigs = self.h1x_gwss_contig(
             contig=contig,
             analysis=analysis,
             window_size=window_size,
@@ -232,23 +335,30 @@ def plot_h1x_gwss_track(
             output_backend=output_backend,
         )
 
-        circle_kwargs_mutable = dict(circle_kwargs) if circle_kwargs else {}
-        circle_kwargs_mutable["size"] = circle_kwargs_mutable.get("size", 3)
-        circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get("line_width", 1)
-        circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
-            "line_color", "black"
-        )
-        circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
-            "fill_color", None
-        )
-
         # Plot H1X.
-        fig.scatter(
-            x=x,
-            y=h1x,
-            marker="circle",
-            **circle_kwargs_mutable,
-        )
+        for s in set(contigs):
+            idxs = contigs == s
+            circle_kwargs_mutable = (
+                dict(circle_kwargs_dict[s]) if circle_kwargs_dict else {}
+            )
+            circle_kwargs_mutable["size"] = circle_kwargs_mutable.get(
+                "size", gplt_params.default_circle_kwargs_dict[s]["size"]
+            )
+            circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get(
+                "line_width", gplt_params.default_circle_kwargs_dict[s]["line_width"]
+            )
+            circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
+                "line_color", gplt_params.default_circle_kwargs_dict[s]["line_color"]
+            )
+            circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
+                "fill_color", gplt_params.default_circle_kwargs_dict[s]["fill_color"]
+            )
+            fig.scatter(
+                x=x[idxs],
+                y=h1x[idxs],
+                marker="circle",
+                **circle_kwargs_mutable,
+            )
 
         # Tidy up the plot.
         fig.yaxis.axis_label = "H1X"
@@ -288,7 +398,7 @@ def plot_h1x_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 190,
-        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
+        circle_kwargs_dict: Optional[gplt_params.circle_kwargs_dict] = None,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -311,7 +421,7 @@ def plot_h1x_gwss(
             sizing_mode=sizing_mode,
             width=width,
             height=track_height,
-            circle_kwargs=circle_kwargs,
+            circle_kwargs_dict=circle_kwargs_dict,
             show=False,
             output_backend=output_backend,
             chunks=chunks,
diff --git a/tests/anoph/test_h1x.py b/tests/anoph/test_h1x.py
index 47720a76b..b1e982036 100644
--- a/tests/anoph/test_h1x.py
+++ b/tests/anoph/test_h1x.py
@@ -123,10 +123,20 @@ def check_h1x_gwss(*, api, h1x_params):
     assert np.all(h1x >= 0)
     assert np.all(h1x <= 1)
 
+    circle_kwargs_dict = {
+        0: {"line_color": "black", "size": 5, "line_width": 1, "fill_color": None},
+        1: {"line_color": "green", "size": 4, "line_width": 2, "fill_color": "black"},
+        2: {"line_color": "orange", "size": 3, "line_width": 1, "fill_color": None},
+        3: {"line_color": "green", "size": 2, "line_width": 2, "fill_color": "black"},
+        4: {"line_color": "purple", "size": 1, "line_width": 1, "fill_color": None},
+    }
+
     # Check plotting functions.
     fig = api.plot_h1x_gwss_track(**h1x_params, show=False)
     assert isinstance(fig, bokeh.models.Plot)
-    fig = api.plot_h1x_gwss(**h1x_params, show=False)
+    fig = api.plot_h1x_gwss(
+        **h1x_params, circle_kwargs_dict=circle_kwargs_dict, show=False
+    )
     assert isinstance(fig, bokeh.models.GridPlot)
 
 

From 20947b3c647691e49b2bb249997789823134ebde Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Thu, 3 Oct 2024 14:00:35 +0100
Subject: [PATCH 18/33] Gave the users more options.

---
 malariagen_data/anoph/gplt_params.py |  10 +++
 malariagen_data/anoph/h12.py         | 113 ++++++++++++++++++++++-----
 malariagen_data/anoph/h1x.py         | 113 ++++++++++++++++++++++-----
 tests/anoph/test_h12.py              |   4 +-
 tests/anoph/test_h1x.py              |   2 +-
 5 files changed, 203 insertions(+), 39 deletions(-)

diff --git a/malariagen_data/anoph/gplt_params.py b/malariagen_data/anoph/gplt_params.py
index 90d93ac97..5a3f7009c 100644
--- a/malariagen_data/anoph/gplt_params.py
+++ b/malariagen_data/anoph/gplt_params.py
@@ -116,3 +116,13 @@
     3: {"line_color": "green", "size": 3, "line_width": 1, "fill_color": None},
     4: {"line_color": "purple", "size": 3, "line_width": 1, "fill_color": None},
 }
+
+circle_kwargs_list: TypeAlias = Annotated[
+    list[circle_kwargs],
+    "A list of arguments passed through to bokeh scatter() function with marker = 'circle' with a value per contig.",
+]
+
+circle_kwargs_param: TypeAlias = Annotated[
+    Union[circle_kwargs, circle_kwargs_dict, circle_kwargs_list],
+    "A set of arguments passed through to bokeh scatter() function with marker = 'circle'.",
+]
diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 2f71f80b5..4aba93744 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -438,7 +438,7 @@ def plot_h12_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
-        circle_kwargs_dict: Optional[gplt_params.circle_kwargs_dict] = None,
+        circle_kwargs_param: Optional[gplt_params.circle_kwargs_param] = None,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -460,6 +460,97 @@ def plot_h12_gwss_track(
             inline_array=inline_array,
         )
 
+        if circle_kwargs_param is None:
+            circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
+        elif isinstance(circle_kwargs_param, list):
+            if len(circle_kwargs_param) >= 5:
+                circle_kwargs_param_dict = {
+                    i: circle_kwargs_param[i] for i in range(0, 5)
+                }
+            else:
+                circle_kwargs_param_dict = {
+                    i: circle_kwargs_param[i]
+                    for i in range(0, len(circle_kwargs_param))
+                }
+                circle_kwargs_param_dict.update(
+                    {
+                        i: gplt_params.default_circle_kwargs_dict[i]
+                        for i in range(len(circle_kwargs_param), 5)
+                    }
+                )
+        elif isinstance(circle_kwargs_param, dict):
+            if isinstance(list(circle_kwargs_param.keys())[0], str):
+                if list(circle_kwargs_param.keys())[0] in [
+                    "2L",
+                    "2R",
+                    "3L",
+                    "3R",
+                    "X",
+                    "2RL",
+                    "3RL",
+                ]:
+                    circle_kwargs_param_dict = {}
+                    for i in range(0, 5):
+                        if i == 0:
+                            if "2L" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["2L"]
+                            elif "2RL" in circle_kwargs_param.keys():  # Af1
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["2RL"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 1:
+                            if "2R" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["2R"]
+                            elif "3RL" in circle_kwargs_param.keys():  # Af1
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["3RL"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 2:
+                            if "3L" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["3L"]
+                            elif "X" in circle_kwargs_param.keys():  # Af1
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 3:
+                            if "3R" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["3R"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 4:
+                            if (
+                                "X" in circle_kwargs_param.keys()
+                            ):  # Ag3. Will also get a value for Af1 but it will be ignored.
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                else:
+                    print("circle_kwargs")
+                    circle_kwargs_param_dict = {
+                        i: circle_kwargs_param for i in range(0, 5)
+                    }
+            elif isinstance(list(circle_kwargs_param.keys())[0], int):
+                circle_kwargs_param_dict = {}
+                for i in range(0, 5):
+                    if i in list(circle_kwargs_param.keys()):
+                        circle_kwargs_param_dict[i] = circle_kwargs_param[i]
+                    else:
+                        circle_kwargs_param_dict[
+                            i
+                        ] = gplt_params.default_circle_kwargs_dict[i]
+        else:
+            circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
+
         # Determine X axis range.
         x_min = x[0]
         x_max = x[-1]
@@ -498,21 +589,7 @@ def plot_h12_gwss_track(
         # Plot H12.
         for s in set(contigs):
             idxs = contigs == s
-            circle_kwargs_mutable = (
-                dict(circle_kwargs_dict[s]) if circle_kwargs_dict else {}
-            )
-            circle_kwargs_mutable["size"] = circle_kwargs_mutable.get(
-                "size", gplt_params.default_circle_kwargs_dict[s]["size"]
-            )
-            circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get(
-                "line_width", gplt_params.default_circle_kwargs_dict[s]["line_width"]
-            )
-            circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
-                "line_color", gplt_params.default_circle_kwargs_dict[s]["line_color"]
-            )
-            circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
-                "fill_color", gplt_params.default_circle_kwargs_dict[s]["fill_color"]
-            )
+            circle_kwargs_mutable = circle_kwargs_param_dict[s]
             fig.scatter(
                 x=x[idxs],
                 y=h12[idxs],
@@ -554,7 +631,7 @@ def plot_h12_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 170,
-        circle_kwargs_dict: Optional[gplt_params.circle_kwargs_dict] = None,
+        circle_kwargs_param: Optional[gplt_params.circle_kwargs_param] = None,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -576,7 +653,7 @@ def plot_h12_gwss(
             sizing_mode=sizing_mode,
             width=width,
             height=track_height,
-            circle_kwargs_dict=circle_kwargs_dict,
+            circle_kwargs_param=circle_kwargs_param,
             show=False,
             output_backend=output_backend,
             chunks=chunks,
diff --git a/malariagen_data/anoph/h1x.py b/malariagen_data/anoph/h1x.py
index 994728b10..86c41b307 100644
--- a/malariagen_data/anoph/h1x.py
+++ b/malariagen_data/anoph/h1x.py
@@ -277,7 +277,7 @@ def plot_h1x_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
-        circle_kwargs_dict: Optional[gplt_params.circle_kwargs_dict] = None,
+        circle_kwargs_param: Optional[gplt_params.circle_kwargs_param] = None,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -300,6 +300,97 @@ def plot_h1x_gwss_track(
             inline_array=inline_array,
         )
 
+        if circle_kwargs_param is None:
+            circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
+        elif isinstance(circle_kwargs_param, list):
+            if len(circle_kwargs_param) >= 5:
+                circle_kwargs_param_dict = {
+                    i: circle_kwargs_param[i] for i in range(0, 5)
+                }
+            else:
+                circle_kwargs_param_dict = {
+                    i: circle_kwargs_param[i]
+                    for i in range(0, len(circle_kwargs_param))
+                }
+                circle_kwargs_param_dict.update(
+                    {
+                        i: gplt_params.default_circle_kwargs_dict[i]
+                        for i in range(len(circle_kwargs_param), 5)
+                    }
+                )
+        elif isinstance(circle_kwargs_param, dict):
+            if isinstance(list(circle_kwargs_param.keys())[0], str):
+                if list(circle_kwargs_param.keys())[0] in [
+                    "2L",
+                    "2R",
+                    "3L",
+                    "3R",
+                    "X",
+                    "2RL",
+                    "3RL",
+                ]:
+                    circle_kwargs_param_dict = {}
+                    for i in range(0, 5):
+                        if i == 0:
+                            if "2L" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["2L"]
+                            elif "2RL" in circle_kwargs_param.keys():  # Af1
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["2RL"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 1:
+                            if "2R" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["2R"]
+                            elif "3RL" in circle_kwargs_param.keys():  # Af1
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["3RL"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 2:
+                            if "3L" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["3L"]
+                            elif "X" in circle_kwargs_param.keys():  # Af1
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 3:
+                            if "3R" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["3R"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 4:
+                            if (
+                                "X" in circle_kwargs_param.keys()
+                            ):  # Ag3. Will also get a value for Af1 but it will be ignored.
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                else:
+                    print("circle_kwargs")
+                    circle_kwargs_param_dict = {
+                        i: circle_kwargs_param for i in range(0, 5)
+                    }
+            elif isinstance(list(circle_kwargs_param.keys())[0], int):
+                circle_kwargs_param_dict = {}
+                for i in range(0, 5):
+                    if i in list(circle_kwargs_param.keys()):
+                        circle_kwargs_param_dict[i] = circle_kwargs_param[i]
+                    else:
+                        circle_kwargs_param_dict[
+                            i
+                        ] = gplt_params.default_circle_kwargs_dict[i]
+        else:
+            circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
+
         # Determine X axis range.
         x_min = x[0]
         x_max = x[-1]
@@ -338,21 +429,7 @@ def plot_h1x_gwss_track(
         # Plot H1X.
         for s in set(contigs):
             idxs = contigs == s
-            circle_kwargs_mutable = (
-                dict(circle_kwargs_dict[s]) if circle_kwargs_dict else {}
-            )
-            circle_kwargs_mutable["size"] = circle_kwargs_mutable.get(
-                "size", gplt_params.default_circle_kwargs_dict[s]["size"]
-            )
-            circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get(
-                "line_width", gplt_params.default_circle_kwargs_dict[s]["line_width"]
-            )
-            circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
-                "line_color", gplt_params.default_circle_kwargs_dict[s]["line_color"]
-            )
-            circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
-                "fill_color", gplt_params.default_circle_kwargs_dict[s]["fill_color"]
-            )
+            circle_kwargs_mutable = circle_kwargs_param_dict[s]
             fig.scatter(
                 x=x[idxs],
                 y=h1x[idxs],
@@ -398,7 +475,7 @@ def plot_h1x_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 190,
-        circle_kwargs_dict: Optional[gplt_params.circle_kwargs_dict] = None,
+        circle_kwargs_param: Optional[gplt_params.circle_kwargs_param] = None,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -421,7 +498,7 @@ def plot_h1x_gwss(
             sizing_mode=sizing_mode,
             width=width,
             height=track_height,
-            circle_kwargs_dict=circle_kwargs_dict,
+            circle_kwargs_param=circle_kwargs_param,
             show=False,
             output_backend=output_backend,
             chunks=chunks,
diff --git a/tests/anoph/test_h12.py b/tests/anoph/test_h12.py
index b516b88eb..7e7490b97 100644
--- a/tests/anoph/test_h12.py
+++ b/tests/anoph/test_h12.py
@@ -152,11 +152,11 @@ def check_h12_gwss(*, api, h12_params):
 
     # Check plotting functions.
     fig = api.plot_h12_gwss_track(
-        **h12_params, circle_kwargs_dict=circle_kwargs_dict, show=False
+        **h12_params, circle_kwargs_param=circle_kwargs_dict, show=False
     )
     assert isinstance(fig, bokeh.models.Plot)
     fig = api.plot_h12_gwss(
-        **h12_params, circle_kwargs_dict=circle_kwargs_dict, show=False
+        **h12_params, circle_kwargs_param=circle_kwargs_dict[0], show=False
     )
     assert isinstance(fig, bokeh.models.GridPlot)
 
diff --git a/tests/anoph/test_h1x.py b/tests/anoph/test_h1x.py
index b1e982036..3f759a13c 100644
--- a/tests/anoph/test_h1x.py
+++ b/tests/anoph/test_h1x.py
@@ -135,7 +135,7 @@ def check_h1x_gwss(*, api, h1x_params):
     fig = api.plot_h1x_gwss_track(**h1x_params, show=False)
     assert isinstance(fig, bokeh.models.Plot)
     fig = api.plot_h1x_gwss(
-        **h1x_params, circle_kwargs_dict=circle_kwargs_dict, show=False
+        **h1x_params, circle_kwargs_param=circle_kwargs_dict, show=False
     )
     assert isinstance(fig, bokeh.models.GridPlot)
 

From 5f84b9d70c692a350629e5b475276b612ba01ec4 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Thu, 3 Oct 2024 14:36:30 +0100
Subject: [PATCH 19/33] Refining a type to defeat linting.

---
 malariagen_data/anoph/gplt_params.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/malariagen_data/anoph/gplt_params.py b/malariagen_data/anoph/gplt_params.py
index 5a3f7009c..9e8ac9bcf 100644
--- a/malariagen_data/anoph/gplt_params.py
+++ b/malariagen_data/anoph/gplt_params.py
@@ -105,7 +105,7 @@
 ]
 
 circle_kwargs_dict: TypeAlias = Annotated[
-    dict[int, circle_kwargs],
+    Union[dict[int, circle_kwargs], dict[str, circle_kwargs]],
     "A dictionary of arguments passed through to bokeh scatter() function with marker = 'circle' with a value per contig.",
 ]
 

From 90c5982532500058fa332544e29822265d82cc4c Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Thu, 3 Oct 2024 14:48:51 +0100
Subject: [PATCH 20/33] Same problem, different solution.

---
 malariagen_data/anoph/h12.py | 2 +-
 malariagen_data/anoph/h1x.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 4aba93744..70761f4ef 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -489,7 +489,7 @@ def plot_h12_gwss_track(
                     "2RL",
                     "3RL",
                 ]:
-                    circle_kwargs_param_dict = {}
+                    circle_kwargs_param_dict: dict[int, gplt_params.circle_kwargs] = {}
                     for i in range(0, 5):
                         if i == 0:
                             if "2L" in circle_kwargs_param.keys():  # Ag3
diff --git a/malariagen_data/anoph/h1x.py b/malariagen_data/anoph/h1x.py
index 86c41b307..8689112bd 100644
--- a/malariagen_data/anoph/h1x.py
+++ b/malariagen_data/anoph/h1x.py
@@ -329,7 +329,7 @@ def plot_h1x_gwss_track(
                     "2RL",
                     "3RL",
                 ]:
-                    circle_kwargs_param_dict = {}
+                    circle_kwargs_param_dict: dict[int, gplt_params.circle_kwargs] = {}
                     for i in range(0, 5):
                         if i == 0:
                             if "2L" in circle_kwargs_param.keys():  # Ag3

From 528d3ec91b5119b94ec053822398f6b5f25a106b Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Thu, 3 Oct 2024 14:54:57 +0100
Subject: [PATCH 21/33] Same problem, not s different solution.

---
 malariagen_data/anoph/h12.py | 2 +-
 malariagen_data/anoph/h1x.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 70761f4ef..b5f413515 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -460,6 +460,7 @@ def plot_h12_gwss_track(
             inline_array=inline_array,
         )
 
+        circle_kwargs_param_dict: dict[int, gplt_params.circle_kwargs] = {}
         if circle_kwargs_param is None:
             circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
         elif isinstance(circle_kwargs_param, list):
@@ -489,7 +490,6 @@ def plot_h12_gwss_track(
                     "2RL",
                     "3RL",
                 ]:
-                    circle_kwargs_param_dict: dict[int, gplt_params.circle_kwargs] = {}
                     for i in range(0, 5):
                         if i == 0:
                             if "2L" in circle_kwargs_param.keys():  # Ag3
diff --git a/malariagen_data/anoph/h1x.py b/malariagen_data/anoph/h1x.py
index 8689112bd..2a89fbbd1 100644
--- a/malariagen_data/anoph/h1x.py
+++ b/malariagen_data/anoph/h1x.py
@@ -300,6 +300,7 @@ def plot_h1x_gwss_track(
             inline_array=inline_array,
         )
 
+        circle_kwargs_param_dict: dict[int, gplt_params.circle_kwargs] = {}
         if circle_kwargs_param is None:
             circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
         elif isinstance(circle_kwargs_param, list):
@@ -329,7 +330,6 @@ def plot_h1x_gwss_track(
                     "2RL",
                     "3RL",
                 ]:
-                    circle_kwargs_param_dict: dict[int, gplt_params.circle_kwargs] = {}
                     for i in range(0, 5):
                         if i == 0:
                             if "2L" in circle_kwargs_param.keys():  # Ag3

From fdef7ebfa93933a8a55d048627ae25edd928d4a5 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Thu, 3 Oct 2024 14:58:49 +0100
Subject: [PATCH 22/33] Same problem, not a solution.

---
 malariagen_data/anoph/h12.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index b5f413515..d99fb24c8 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -493,9 +493,17 @@ def plot_h12_gwss_track(
                     for i in range(0, 5):
                         if i == 0:
                             if "2L" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["2L"]
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[
+                                    i
+                                ]  # circle_kwargs_param["2L"]
                             elif "2RL" in circle_kwargs_param.keys():  # Af1
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["2RL"]
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[
+                                    i
+                                ]  # circle_kwargs_param["2RL"]
                             else:
                                 circle_kwargs_param_dict[
                                     i

From f141953a0e9ba5fc39e92de45089f1dab8fcb36d Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Thu, 3 Oct 2024 15:03:31 +0100
Subject: [PATCH 23/33] Trying a new idea.

---
 malariagen_data/anoph/h12.py | 147 +++++++++++++++++------------------
 1 file changed, 71 insertions(+), 76 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index d99fb24c8..bf744af42 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -479,83 +479,78 @@ def plot_h12_gwss_track(
                         for i in range(len(circle_kwargs_param), 5)
                     }
                 )
-        elif isinstance(circle_kwargs_param, dict):
-            if isinstance(list(circle_kwargs_param.keys())[0], str):
-                if list(circle_kwargs_param.keys())[0] in [
-                    "2L",
-                    "2R",
-                    "3L",
-                    "3R",
-                    "X",
-                    "2RL",
-                    "3RL",
-                ]:
-                    for i in range(0, 5):
-                        if i == 0:
-                            if "2L" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[
-                                    i
-                                ]  # circle_kwargs_param["2L"]
-                            elif "2RL" in circle_kwargs_param.keys():  # Af1
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[
-                                    i
-                                ]  # circle_kwargs_param["2RL"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 1:
-                            if "2R" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["2R"]
-                            elif "3RL" in circle_kwargs_param.keys():  # Af1
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["3RL"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 2:
-                            if "3L" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["3L"]
-                            elif "X" in circle_kwargs_param.keys():  # Af1
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 3:
-                            if "3R" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["3R"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 4:
-                            if (
-                                "X" in circle_kwargs_param.keys()
-                            ):  # Ag3. Will also get a value for Af1 but it will be ignored.
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                else:
-                    print("circle_kwargs")
-                    circle_kwargs_param_dict = {
-                        i: circle_kwargs_param for i in range(0, 5)
-                    }
-            elif isinstance(list(circle_kwargs_param.keys())[0], int):
-                circle_kwargs_param_dict = {}
+        elif isinstance(circle_kwargs_param, dict[str, dict]):
+            if list(circle_kwargs_param.keys())[0] in [
+                "2L",
+                "2R",
+                "3L",
+                "3R",
+                "X",
+                "2RL",
+                "3RL",
+            ]:
                 for i in range(0, 5):
-                    if i in list(circle_kwargs_param.keys()):
-                        circle_kwargs_param_dict[i] = circle_kwargs_param[i]
-                    else:
-                        circle_kwargs_param_dict[
-                            i
-                        ] = gplt_params.default_circle_kwargs_dict[i]
+                    if i == 0:
+                        if "2L" in circle_kwargs_param.keys():  # Ag3
+                            circle_kwargs_param_dict[
+                                i
+                            ] = gplt_params.default_circle_kwargs_dict[
+                                i
+                            ]  # circle_kwargs_param["2L"]
+                        elif "2RL" in circle_kwargs_param.keys():  # Af1
+                            circle_kwargs_param_dict[
+                                i
+                            ] = gplt_params.default_circle_kwargs_dict[
+                                i
+                            ]  # circle_kwargs_param["2RL"]
+                        else:
+                            circle_kwargs_param_dict[
+                                i
+                            ] = gplt_params.default_circle_kwargs_dict[i]
+                    elif i == 1:
+                        if "2R" in circle_kwargs_param.keys():  # Ag3
+                            circle_kwargs_param_dict[i] = circle_kwargs_param["2R"]
+                        elif "3RL" in circle_kwargs_param.keys():  # Af1
+                            circle_kwargs_param_dict[i] = circle_kwargs_param["3RL"]
+                        else:
+                            circle_kwargs_param_dict[
+                                i
+                            ] = gplt_params.default_circle_kwargs_dict[i]
+                    elif i == 2:
+                        if "3L" in circle_kwargs_param.keys():  # Ag3
+                            circle_kwargs_param_dict[i] = circle_kwargs_param["3L"]
+                        elif "X" in circle_kwargs_param.keys():  # Af1
+                            circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
+                        else:
+                            circle_kwargs_param_dict[
+                                i
+                            ] = gplt_params.default_circle_kwargs_dict[i]
+                    elif i == 3:
+                        if "3R" in circle_kwargs_param.keys():  # Ag3
+                            circle_kwargs_param_dict[i] = circle_kwargs_param["3R"]
+                        else:
+                            circle_kwargs_param_dict[
+                                i
+                            ] = gplt_params.default_circle_kwargs_dict[i]
+                    elif i == 4:
+                        if (
+                            "X" in circle_kwargs_param.keys()
+                        ):  # Ag3. Will also get a value for Af1 but it will be ignored.
+                            circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
+                        else:
+                            circle_kwargs_param_dict[
+                                i
+                            ] = gplt_params.default_circle_kwargs_dict[i]
+            else:
+                circle_kwargs_param_dict = {i: circle_kwargs_param for i in range(0, 5)}
+        elif isinstance(circle_kwargs_param, dict[int, dict]):
+            for i in range(0, 5):
+                if i in list(circle_kwargs_param.keys()):
+                    circle_kwargs_param_dict[i] = circle_kwargs_param[i]
+                else:
+                    circle_kwargs_param_dict[
+                        i
+                    ] = gplt_params.default_circle_kwargs_dict[i]
         else:
             circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
 

From 2e34ff15abe5ed0c1eabbeef8bac6a48ead3c42c Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Thu, 3 Oct 2024 15:10:28 +0100
Subject: [PATCH 24/33] Going the opposite way.

---
 malariagen_data/anoph/h12.py | 142 +++++++++++++++++------------------
 1 file changed, 71 insertions(+), 71 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index bf744af42..dc0a22efc 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -479,78 +479,78 @@ def plot_h12_gwss_track(
                         for i in range(len(circle_kwargs_param), 5)
                     }
                 )
-        elif isinstance(circle_kwargs_param, dict[str, dict]):
-            if list(circle_kwargs_param.keys())[0] in [
-                "2L",
-                "2R",
-                "3L",
-                "3R",
-                "X",
-                "2RL",
-                "3RL",
-            ]:
-                for i in range(0, 5):
-                    if i == 0:
-                        if "2L" in circle_kwargs_param.keys():  # Ag3
-                            circle_kwargs_param_dict[
-                                i
-                            ] = gplt_params.default_circle_kwargs_dict[
-                                i
-                            ]  # circle_kwargs_param["2L"]
-                        elif "2RL" in circle_kwargs_param.keys():  # Af1
-                            circle_kwargs_param_dict[
-                                i
-                            ] = gplt_params.default_circle_kwargs_dict[
-                                i
-                            ]  # circle_kwargs_param["2RL"]
-                        else:
-                            circle_kwargs_param_dict[
-                                i
-                            ] = gplt_params.default_circle_kwargs_dict[i]
-                    elif i == 1:
-                        if "2R" in circle_kwargs_param.keys():  # Ag3
-                            circle_kwargs_param_dict[i] = circle_kwargs_param["2R"]
-                        elif "3RL" in circle_kwargs_param.keys():  # Af1
-                            circle_kwargs_param_dict[i] = circle_kwargs_param["3RL"]
-                        else:
-                            circle_kwargs_param_dict[
-                                i
-                            ] = gplt_params.default_circle_kwargs_dict[i]
-                    elif i == 2:
-                        if "3L" in circle_kwargs_param.keys():  # Ag3
-                            circle_kwargs_param_dict[i] = circle_kwargs_param["3L"]
-                        elif "X" in circle_kwargs_param.keys():  # Af1
-                            circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
-                        else:
-                            circle_kwargs_param_dict[
-                                i
-                            ] = gplt_params.default_circle_kwargs_dict[i]
-                    elif i == 3:
-                        if "3R" in circle_kwargs_param.keys():  # Ag3
-                            circle_kwargs_param_dict[i] = circle_kwargs_param["3R"]
-                        else:
-                            circle_kwargs_param_dict[
-                                i
-                            ] = gplt_params.default_circle_kwargs_dict[i]
-                    elif i == 4:
-                        if (
-                            "X" in circle_kwargs_param.keys()
-                        ):  # Ag3. Will also get a value for Af1 but it will be ignored.
-                            circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
-                        else:
-                            circle_kwargs_param_dict[
-                                i
-                            ] = gplt_params.default_circle_kwargs_dict[i]
-            else:
-                circle_kwargs_param_dict = {i: circle_kwargs_param for i in range(0, 5)}
-        elif isinstance(circle_kwargs_param, dict[int, dict]):
-            for i in range(0, 5):
-                if i in list(circle_kwargs_param.keys()):
-                    circle_kwargs_param_dict[i] = circle_kwargs_param[i]
+        elif isinstance(circle_kwargs_param, dict):
+            if isinstance(list(circle_kwargs_param.keys())[0], str):
+                if list(circle_kwargs_param.keys())[0] in [
+                    "2L",
+                    "2R",
+                    "3L",
+                    "3R",
+                    "X",
+                    "2RL",
+                    "3RL",
+                ]:
+                    for i in range(0, 5):
+                        if i == 0:
+                            ck = circle_kwargs_param["2L"]
+                            if "2L" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = ck
+                            elif "2RL" in circle_kwargs_param.keys():  # Af1
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[
+                                    i
+                                ]  # circle_kwargs_param["2RL"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 1:
+                            if "2R" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["2R"]
+                            elif "3RL" in circle_kwargs_param.keys():  # Af1
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["3RL"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 2:
+                            if "3L" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["3L"]
+                            elif "X" in circle_kwargs_param.keys():  # Af1
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 3:
+                            if "3R" in circle_kwargs_param.keys():  # Ag3
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["3R"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
+                        elif i == 4:
+                            if (
+                                "X" in circle_kwargs_param.keys()
+                            ):  # Ag3. Will also get a value for Af1 but it will be ignored.
+                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
+                            else:
+                                circle_kwargs_param_dict[
+                                    i
+                                ] = gplt_params.default_circle_kwargs_dict[i]
                 else:
-                    circle_kwargs_param_dict[
-                        i
-                    ] = gplt_params.default_circle_kwargs_dict[i]
+                    circle_kwargs_param_dict = {
+                        i: circle_kwargs_param for i in range(0, 5)
+                    }
+            elif isinstance(list(circle_kwargs_param.keys())[0], int):
+                for i in range(0, 5):
+                    if i in list(circle_kwargs_param.keys()):
+                        circle_kwargs_param_dict[i] = circle_kwargs_param[i]
+                    else:
+                        circle_kwargs_param_dict[
+                            i
+                        ] = gplt_params.default_circle_kwargs_dict[i]
         else:
             circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
 

From ff544057908e4aa6fe2c11895ae948f6b663e804 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Thu, 3 Oct 2024 16:27:36 +0100
Subject: [PATCH 25/33] More tests.

---
 tests/anoph/test_h1x.py | 20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/tests/anoph/test_h1x.py b/tests/anoph/test_h1x.py
index 3f759a13c..020c46ae1 100644
--- a/tests/anoph/test_h1x.py
+++ b/tests/anoph/test_h1x.py
@@ -124,11 +124,21 @@ def check_h1x_gwss(*, api, h1x_params):
     assert np.all(h1x <= 1)
 
     circle_kwargs_dict = {
-        0: {"line_color": "black", "size": 5, "line_width": 1, "fill_color": None},
-        1: {"line_color": "green", "size": 4, "line_width": 2, "fill_color": "black"},
-        2: {"line_color": "orange", "size": 3, "line_width": 1, "fill_color": None},
-        3: {"line_color": "green", "size": 2, "line_width": 2, "fill_color": "black"},
-        4: {"line_color": "purple", "size": 1, "line_width": 1, "fill_color": None},
+        "2L": {"line_color": "black", "size": 5, "line_width": 1, "fill_color": None},
+        "2R": {
+            "line_color": "green",
+            "size": 4,
+            "line_width": 2,
+            "fill_color": "black",
+        },
+        "3L": {"line_color": "orange", "size": 3, "line_width": 1, "fill_color": None},
+        "3R": {
+            "line_color": "green",
+            "size": 2,
+            "line_width": 2,
+            "fill_color": "black",
+        },
+        "X": {"line_color": "purple", "size": 1, "line_width": 1, "fill_color": None},
     }
 
     # Check plotting functions.

From f98d6017fcd0e1ed14a939a63e4c765ad081abb4 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 7 Oct 2024 16:08:44 +0100
Subject: [PATCH 26/33] Simplified everything

---
 malariagen_data/anoph/gplt_params.py |  21 ++---
 malariagen_data/anoph/h12.py         | 116 ++++-----------------------
 malariagen_data/anoph/h1x.py         | 113 ++++----------------------
 tests/anoph/test_h12.py              |  31 ++++---
 tests/anoph/test_h1x.py              |  37 ++++-----
 5 files changed, 70 insertions(+), 248 deletions(-)

diff --git a/malariagen_data/anoph/gplt_params.py b/malariagen_data/anoph/gplt_params.py
index 9e8ac9bcf..9221dd4d9 100644
--- a/malariagen_data/anoph/gplt_params.py
+++ b/malariagen_data/anoph/gplt_params.py
@@ -1,7 +1,7 @@
 """Parameters for genome plotting functions. N.B., genome plots are always
 plotted with bokeh."""
 
-from typing import Literal, Mapping, Optional, Union, Final
+from typing import Literal, Mapping, Optional, Union, Final, Sequence
 
 import bokeh.models
 from typing_extensions import Annotated, TypeAlias
@@ -109,20 +109,9 @@
     "A dictionary of arguments passed through to bokeh scatter() function with marker = 'circle' with a value per contig.",
 ]
 
-default_circle_kwargs_dict: Final[dict[int, circle_kwargs]] = {
-    0: {"line_color": "red", "size": 3, "line_width": 1, "fill_color": None},
-    1: {"line_color": "blue", "size": 3, "line_width": 1, "fill_color": None},
-    2: {"line_color": "orange", "size": 3, "line_width": 1, "fill_color": None},
-    3: {"line_color": "green", "size": 3, "line_width": 1, "fill_color": None},
-    4: {"line_color": "purple", "size": 3, "line_width": 1, "fill_color": None},
-}
-
-circle_kwargs_list: TypeAlias = Annotated[
-    list[circle_kwargs],
-    "A list of arguments passed through to bokeh scatter() function with marker = 'circle' with a value per contig.",
+contig_colors: TypeAlias = Annotated[
+    Sequence[str],
+    "A sequence of colors.",
 ]
 
-circle_kwargs_param: TypeAlias = Annotated[
-    Union[circle_kwargs, circle_kwargs_dict, circle_kwargs_list],
-    "A set of arguments passed through to bokeh scatter() function with marker = 'circle'.",
-]
+contig_colors_default: Final[contig_colors] = bokeh.palettes.d3["Category20b"][5]
diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index dc0a22efc..241804e6c 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -258,8 +258,13 @@ def _h12_gwss_contig(
             # Compute window midpoints.
             pos = ds_haps["variant_position"].values
             x = allel.moving_statistic(pos, statistic=np.mean, size=window_size)
-            contigs = allel.moving_statistic(
-                ds_haps["variant_contig"].values, statistic=np.median, size=window_size
+            contigs = np.asarray(
+                allel.moving_statistic(
+                    ds_haps["variant_contig"].values,
+                    statistic=np.median,
+                    size=window_size,
+                ),
+                dtype=int,
             )
 
         results = dict(x=x, h12=h12, contigs=contigs)
@@ -438,7 +443,9 @@ def plot_h12_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
-        circle_kwargs_param: Optional[gplt_params.circle_kwargs_param] = None,
+        contig_colors: Optional[
+            gplt_params.contig_colors
+        ] = gplt_params.contig_colors_default,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -460,100 +467,6 @@ def plot_h12_gwss_track(
             inline_array=inline_array,
         )
 
-        circle_kwargs_param_dict: dict[int, gplt_params.circle_kwargs] = {}
-        if circle_kwargs_param is None:
-            circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
-        elif isinstance(circle_kwargs_param, list):
-            if len(circle_kwargs_param) >= 5:
-                circle_kwargs_param_dict = {
-                    i: circle_kwargs_param[i] for i in range(0, 5)
-                }
-            else:
-                circle_kwargs_param_dict = {
-                    i: circle_kwargs_param[i]
-                    for i in range(0, len(circle_kwargs_param))
-                }
-                circle_kwargs_param_dict.update(
-                    {
-                        i: gplt_params.default_circle_kwargs_dict[i]
-                        for i in range(len(circle_kwargs_param), 5)
-                    }
-                )
-        elif isinstance(circle_kwargs_param, dict):
-            if isinstance(list(circle_kwargs_param.keys())[0], str):
-                if list(circle_kwargs_param.keys())[0] in [
-                    "2L",
-                    "2R",
-                    "3L",
-                    "3R",
-                    "X",
-                    "2RL",
-                    "3RL",
-                ]:
-                    for i in range(0, 5):
-                        if i == 0:
-                            ck = circle_kwargs_param["2L"]
-                            if "2L" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = ck
-                            elif "2RL" in circle_kwargs_param.keys():  # Af1
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[
-                                    i
-                                ]  # circle_kwargs_param["2RL"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 1:
-                            if "2R" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["2R"]
-                            elif "3RL" in circle_kwargs_param.keys():  # Af1
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["3RL"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 2:
-                            if "3L" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["3L"]
-                            elif "X" in circle_kwargs_param.keys():  # Af1
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 3:
-                            if "3R" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["3R"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 4:
-                            if (
-                                "X" in circle_kwargs_param.keys()
-                            ):  # Ag3. Will also get a value for Af1 but it will be ignored.
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                else:
-                    circle_kwargs_param_dict = {
-                        i: circle_kwargs_param for i in range(0, 5)
-                    }
-            elif isinstance(list(circle_kwargs_param.keys())[0], int):
-                for i in range(0, 5):
-                    if i in list(circle_kwargs_param.keys()):
-                        circle_kwargs_param_dict[i] = circle_kwargs_param[i]
-                    else:
-                        circle_kwargs_param_dict[
-                            i
-                        ] = gplt_params.default_circle_kwargs_dict[i]
-        else:
-            circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
-
         # Determine X axis range.
         x_min = x[0]
         x_max = x[-1]
@@ -592,12 +505,11 @@ def plot_h12_gwss_track(
         # Plot H12.
         for s in set(contigs):
             idxs = contigs == s
-            circle_kwargs_mutable = circle_kwargs_param_dict[s]
             fig.scatter(
                 x=x[idxs],
                 y=h12[idxs],
                 marker="circle",
-                **circle_kwargs_mutable,
+                color=contig_colors[s % len(contig_colors)],
             )
 
         # Tidy up the plot.
@@ -634,7 +546,9 @@ def plot_h12_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 170,
-        circle_kwargs_param: Optional[gplt_params.circle_kwargs_param] = None,
+        contig_colors: Optional[
+            gplt_params.contig_colors
+        ] = gplt_params.contig_colors_default,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -656,7 +570,7 @@ def plot_h12_gwss(
             sizing_mode=sizing_mode,
             width=width,
             height=track_height,
-            circle_kwargs_param=circle_kwargs_param,
+            contig_colors=contig_colors,
             show=False,
             output_backend=output_backend,
             chunks=chunks,
diff --git a/malariagen_data/anoph/h1x.py b/malariagen_data/anoph/h1x.py
index 2a89fbbd1..16dfc5bed 100644
--- a/malariagen_data/anoph/h1x.py
+++ b/malariagen_data/anoph/h1x.py
@@ -80,8 +80,13 @@ def _h1x_gwss_contig(
             # Compute window midpoints.
             pos = ds1["variant_position"].values
             x = allel.moving_statistic(pos, statistic=np.mean, size=window_size)
-            contigs = allel.moving_statistic(
-                ds1["variant_contig"].values, statistic=np.median, size=window_size
+            contigs = np.asarray(
+                allel.moving_statistic(
+                    ds1["variant_contig"].values,
+                    statistic=np.median,
+                    size=window_size,
+                ),
+                dtype=int,
             )
 
         results = dict(x=x, h1x=h1x, contigs=contigs)
@@ -277,7 +282,9 @@ def plot_h1x_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
-        circle_kwargs_param: Optional[gplt_params.circle_kwargs_param] = None,
+        contig_colors: Optional[
+            gplt_params.contig_colors
+        ] = gplt_params.contig_colors_default,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -300,97 +307,6 @@ def plot_h1x_gwss_track(
             inline_array=inline_array,
         )
 
-        circle_kwargs_param_dict: dict[int, gplt_params.circle_kwargs] = {}
-        if circle_kwargs_param is None:
-            circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
-        elif isinstance(circle_kwargs_param, list):
-            if len(circle_kwargs_param) >= 5:
-                circle_kwargs_param_dict = {
-                    i: circle_kwargs_param[i] for i in range(0, 5)
-                }
-            else:
-                circle_kwargs_param_dict = {
-                    i: circle_kwargs_param[i]
-                    for i in range(0, len(circle_kwargs_param))
-                }
-                circle_kwargs_param_dict.update(
-                    {
-                        i: gplt_params.default_circle_kwargs_dict[i]
-                        for i in range(len(circle_kwargs_param), 5)
-                    }
-                )
-        elif isinstance(circle_kwargs_param, dict):
-            if isinstance(list(circle_kwargs_param.keys())[0], str):
-                if list(circle_kwargs_param.keys())[0] in [
-                    "2L",
-                    "2R",
-                    "3L",
-                    "3R",
-                    "X",
-                    "2RL",
-                    "3RL",
-                ]:
-                    for i in range(0, 5):
-                        if i == 0:
-                            if "2L" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["2L"]
-                            elif "2RL" in circle_kwargs_param.keys():  # Af1
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["2RL"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 1:
-                            if "2R" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["2R"]
-                            elif "3RL" in circle_kwargs_param.keys():  # Af1
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["3RL"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 2:
-                            if "3L" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["3L"]
-                            elif "X" in circle_kwargs_param.keys():  # Af1
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 3:
-                            if "3R" in circle_kwargs_param.keys():  # Ag3
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["3R"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                        elif i == 4:
-                            if (
-                                "X" in circle_kwargs_param.keys()
-                            ):  # Ag3. Will also get a value for Af1 but it will be ignored.
-                                circle_kwargs_param_dict[i] = circle_kwargs_param["X"]
-                            else:
-                                circle_kwargs_param_dict[
-                                    i
-                                ] = gplt_params.default_circle_kwargs_dict[i]
-                else:
-                    print("circle_kwargs")
-                    circle_kwargs_param_dict = {
-                        i: circle_kwargs_param for i in range(0, 5)
-                    }
-            elif isinstance(list(circle_kwargs_param.keys())[0], int):
-                circle_kwargs_param_dict = {}
-                for i in range(0, 5):
-                    if i in list(circle_kwargs_param.keys()):
-                        circle_kwargs_param_dict[i] = circle_kwargs_param[i]
-                    else:
-                        circle_kwargs_param_dict[
-                            i
-                        ] = gplt_params.default_circle_kwargs_dict[i]
-        else:
-            circle_kwargs_param_dict = gplt_params.default_circle_kwargs_dict
-
         # Determine X axis range.
         x_min = x[0]
         x_max = x[-1]
@@ -429,12 +345,11 @@ def plot_h1x_gwss_track(
         # Plot H1X.
         for s in set(contigs):
             idxs = contigs == s
-            circle_kwargs_mutable = circle_kwargs_param_dict[s]
             fig.scatter(
                 x=x[idxs],
                 y=h1x[idxs],
                 marker="circle",
-                **circle_kwargs_mutable,
+                color=contig_colors[s % len(contig_colors)],
             )
 
         # Tidy up the plot.
@@ -475,7 +390,9 @@ def plot_h1x_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 190,
-        circle_kwargs_param: Optional[gplt_params.circle_kwargs_param] = None,
+        contig_colors: Optional[
+            gplt_params.contig_colors
+        ] = gplt_params.contig_colors_default,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -498,7 +415,7 @@ def plot_h1x_gwss(
             sizing_mode=sizing_mode,
             width=width,
             height=track_height,
-            circle_kwargs_param=circle_kwargs_param,
+            contig_colors=contig_colors,
             show=False,
             output_backend=output_backend,
             chunks=chunks,
diff --git a/tests/anoph/test_h12.py b/tests/anoph/test_h12.py
index 7e7490b97..aa0b906a0 100644
--- a/tests/anoph/test_h12.py
+++ b/tests/anoph/test_h12.py
@@ -142,22 +142,27 @@ def check_h12_gwss(*, api, h12_params):
     assert np.all(h12 >= 0)
     assert np.all(h12 <= 1)
 
-    circle_kwargs_dict = {
-        0: {"line_color": "black", "size": 5, "line_width": 1, "fill_color": None},
-        1: {"line_color": "green", "size": 4, "line_width": 2, "fill_color": "black"},
-        2: {"line_color": "orange", "size": 3, "line_width": 1, "fill_color": None},
-        3: {"line_color": "green", "size": 2, "line_width": 2, "fill_color": "black"},
-        4: {"line_color": "purple", "size": 1, "line_width": 1, "fill_color": None},
-    }
+    x, h12, contigs = api.h12_gwss_contig(**h12_params)
+
+    # Check results.
+    assert isinstance(x, np.ndarray)
+    assert isinstance(h12, np.ndarray)
+    assert isinstance(contigs, np.ndarray)
+    assert x.ndim == 1
+    assert h12.ndim == 1
+    assert contigs.ndim == 1
+    assert x.shape == h12.shape
+    assert x.shape == contigs.shape
+    assert x.dtype.kind == "f"
+    assert h12.dtype.kind == "f"
+    assert contigs.dtype.kind == "i"
+    assert np.all(h12 >= 0)
+    assert np.all(h12 <= 1)
 
     # Check plotting functions.
-    fig = api.plot_h12_gwss_track(
-        **h12_params, circle_kwargs_param=circle_kwargs_dict, show=False
-    )
+    fig = api.plot_h12_gwss_track(**h12_params, show=False)
     assert isinstance(fig, bokeh.models.Plot)
-    fig = api.plot_h12_gwss(
-        **h12_params, circle_kwargs_param=circle_kwargs_dict[0], show=False
-    )
+    fig = api.plot_h12_gwss(**h12_params, contig_colors=["black", "red"], show=False)
     assert isinstance(fig, bokeh.models.GridPlot)
 
 
diff --git a/tests/anoph/test_h1x.py b/tests/anoph/test_h1x.py
index 020c46ae1..6cbb0df9e 100644
--- a/tests/anoph/test_h1x.py
+++ b/tests/anoph/test_h1x.py
@@ -123,30 +123,27 @@ def check_h1x_gwss(*, api, h1x_params):
     assert np.all(h1x >= 0)
     assert np.all(h1x <= 1)
 
-    circle_kwargs_dict = {
-        "2L": {"line_color": "black", "size": 5, "line_width": 1, "fill_color": None},
-        "2R": {
-            "line_color": "green",
-            "size": 4,
-            "line_width": 2,
-            "fill_color": "black",
-        },
-        "3L": {"line_color": "orange", "size": 3, "line_width": 1, "fill_color": None},
-        "3R": {
-            "line_color": "green",
-            "size": 2,
-            "line_width": 2,
-            "fill_color": "black",
-        },
-        "X": {"line_color": "purple", "size": 1, "line_width": 1, "fill_color": None},
-    }
+    x, h1x, contigs = api.h1x_gwss_contig(**h1x_params)
+
+    # Check results.
+    assert isinstance(x, np.ndarray)
+    assert isinstance(h1x, np.ndarray)
+    assert isinstance(contigs, np.ndarray)
+    assert x.ndim == 1
+    assert h1x.ndim == 1
+    assert contigs.ndim == 1
+    assert x.shape == h1x.shape
+    assert x.shape == contigs.shape
+    assert x.dtype.kind == "f"
+    assert h1x.dtype.kind == "f"
+    assert contigs.dtype.kind == "i"
+    assert np.all(h1x >= 0)
+    assert np.all(h1x <= 1)
 
     # Check plotting functions.
     fig = api.plot_h1x_gwss_track(**h1x_params, show=False)
     assert isinstance(fig, bokeh.models.Plot)
-    fig = api.plot_h1x_gwss(
-        **h1x_params, circle_kwargs_param=circle_kwargs_dict, show=False
-    )
+    fig = api.plot_h1x_gwss(**h1x_params, contig_colors=["black", "red"], show=False)
     assert isinstance(fig, bokeh.models.GridPlot)
 
 

From 311f5872fdd6667d3a49dfc9e5285193eda6df3b Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 7 Oct 2024 16:15:42 +0100
Subject: [PATCH 27/33] Changed sequence to list

---
 malariagen_data/anoph/gplt_params.py | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/malariagen_data/anoph/gplt_params.py b/malariagen_data/anoph/gplt_params.py
index 9221dd4d9..795dfbfe6 100644
--- a/malariagen_data/anoph/gplt_params.py
+++ b/malariagen_data/anoph/gplt_params.py
@@ -1,7 +1,7 @@
 """Parameters for genome plotting functions. N.B., genome plots are always
 plotted with bokeh."""
 
-from typing import Literal, Mapping, Optional, Union, Final, Sequence
+from typing import Literal, Mapping, Optional, Union, Final
 
 import bokeh.models
 from typing_extensions import Annotated, TypeAlias
@@ -104,14 +104,9 @@
     "Passed through to bokeh line() function.",
 ]
 
-circle_kwargs_dict: TypeAlias = Annotated[
-    Union[dict[int, circle_kwargs], dict[str, circle_kwargs]],
-    "A dictionary of arguments passed through to bokeh scatter() function with marker = 'circle' with a value per contig.",
-]
-
 contig_colors: TypeAlias = Annotated[
-    Sequence[str],
+    list[str],
     "A sequence of colors.",
 ]
 
-contig_colors_default: Final[contig_colors] = bokeh.palettes.d3["Category20b"][5]
+contig_colors_default: Final[contig_colors] = list(bokeh.palettes.d3["Category20b"][5])

From 986004ec6f56c2d5d68dbf1a94a97c27f5dc4c2b Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 7 Oct 2024 16:22:43 +0100
Subject: [PATCH 28/33] Fighting with len

---
 malariagen_data/anoph/h12.py | 8 ++------
 malariagen_data/anoph/h1x.py | 8 ++------
 2 files changed, 4 insertions(+), 12 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 241804e6c..5fc94ffc6 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -443,9 +443,7 @@ def plot_h12_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
-        contig_colors: Optional[
-            gplt_params.contig_colors
-        ] = gplt_params.contig_colors_default,
+        contig_colors: gplt_params.contig_colors = gplt_params.contig_colors_default,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -546,9 +544,7 @@ def plot_h12_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 170,
-        contig_colors: Optional[
-            gplt_params.contig_colors
-        ] = gplt_params.contig_colors_default,
+        contig_colors: gplt_params.contig_colors = gplt_params.contig_colors_default,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
diff --git a/malariagen_data/anoph/h1x.py b/malariagen_data/anoph/h1x.py
index 16dfc5bed..8ce791c64 100644
--- a/malariagen_data/anoph/h1x.py
+++ b/malariagen_data/anoph/h1x.py
@@ -282,9 +282,7 @@ def plot_h1x_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
-        contig_colors: Optional[
-            gplt_params.contig_colors
-        ] = gplt_params.contig_colors_default,
+        contig_colors: gplt_params.contig_colors = gplt_params.contig_colors_default,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -390,9 +388,7 @@ def plot_h1x_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 190,
-        contig_colors: Optional[
-            gplt_params.contig_colors
-        ] = gplt_params.contig_colors_default,
+        contig_colors: gplt_params.contig_colors = gplt_params.contig_colors_default,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,

From bceb950f1f3b6688272519912b84cc28be7302ed Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 7 Oct 2024 16:59:30 +0100
Subject: [PATCH 29/33] Corrected the merge

---
 malariagen_data/anoph/h12.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 1ffaed292..5492b6ba8 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -286,6 +286,7 @@ def _h12_gwss(
         window_size,
         sample_sets,
         sample_query,
+        sample_query_options,
         cohort_size,
         min_cohort_size,
         max_cohort_size,
@@ -299,6 +300,7 @@ def _h12_gwss(
             window_size=window_size,
             sample_query=sample_query,
             sample_sets=sample_sets,
+            sample_query_options=sample_query_options,
             cohort_size=cohort_size,
             min_cohort_size=min_cohort_size,
             max_cohort_size=max_cohort_size,
@@ -325,6 +327,7 @@ def h12_gwss_contig(
         window_size: h12_params.window_size,
         analysis: hap_params.analysis = base_params.DEFAULT,
         sample_query: Optional[base_params.sample_query] = None,
+        sample_query_options: Optional[base_params.sample_query_options] = None,
         sample_sets: Optional[base_params.sample_sets] = None,
         cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default,
         min_cohort_size: Optional[
@@ -350,6 +353,7 @@ def h12_gwss_contig(
             # indices using _prep_sample_selection_params, because the indices
             # are different in the haplotype data.
             sample_query=sample_query,
+            sample_query_options=sample_query_options,
             cohort_size=cohort_size,
             min_cohort_size=min_cohort_size,
             max_cohort_size=max_cohort_size,

From 48fb21e91625e75699c0847be70e7f69b83bda15 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 7 Oct 2024 17:23:42 +0100
Subject: [PATCH 30/33] Returned g123 to its normal state

---
 malariagen_data/anoph/g123.py | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

diff --git a/malariagen_data/anoph/g123.py b/malariagen_data/anoph/g123.py
index 328defc8f..66fde99d0 100644
--- a/malariagen_data/anoph/g123.py
+++ b/malariagen_data/anoph/g123.py
@@ -330,7 +330,6 @@ def plot_g123_gwss_track(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         height: gplt_params.height = 200,
-        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
         show: gplt_params.show = True,
         x_range: Optional[gplt_params.x_range] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -388,22 +387,15 @@ def plot_g123_gwss_track(
             output_backend=output_backend,
         )
 
-        circle_kwargs_mutable = dict(circle_kwargs) if circle_kwargs else {}
-        circle_kwargs_mutable["size"] = circle_kwargs_mutable.get("size", 3)
-        circle_kwargs_mutable["line_width"] = circle_kwargs_mutable.get("line_width", 1)
-        circle_kwargs_mutable["line_color"] = circle_kwargs_mutable.get(
-            "line_color", "black"
-        )
-        circle_kwargs_mutable["fill_color"] = circle_kwargs_mutable.get(
-            "fill_color", None
-        )
-
         # plot G123
         fig.scatter(
             x=x,
             y=g123,
+            size=3,
             marker="circle",
-            **circle_kwargs_mutable,
+            line_width=1,
+            line_color="black",
+            fill_color=None,
         )
 
         # tidy up the plot

From 60780e13b358c93736c8a353e5dea0fb38966d14 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Mon, 7 Oct 2024 17:24:36 +0100
Subject: [PATCH 31/33] Forgot 2 lines

---
 malariagen_data/anoph/g123.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/malariagen_data/anoph/g123.py b/malariagen_data/anoph/g123.py
index 66fde99d0..df6cdc492 100644
--- a/malariagen_data/anoph/g123.py
+++ b/malariagen_data/anoph/g123.py
@@ -433,7 +433,6 @@ def plot_g123_gwss(
         sizing_mode: gplt_params.sizing_mode = gplt_params.sizing_mode_default,
         width: gplt_params.width = gplt_params.width_default,
         track_height: gplt_params.track_height = 170,
-        circle_kwargs: Optional[gplt_params.circle_kwargs] = None,
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
@@ -456,7 +455,6 @@ def plot_g123_gwss(
             sizing_mode=sizing_mode,
             width=width,
             height=track_height,
-            circle_kwargs=circle_kwargs,
             show=False,
             output_backend=output_backend,
             inline_array=inline_array,

From 05a0fcc84a21253db7cf4086bf04a25f185f5bf3 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Sat, 19 Oct 2024 14:56:21 +0100
Subject: [PATCH 32/33] Merged the _contig versions into the main versions

---
 malariagen_data/anoph/h12.py | 102 ++-------------------------------
 malariagen_data/anoph/h1x.py | 106 ++---------------------------------
 tests/anoph/test_h12.py      |  14 +----
 tests/anoph/test_h1x.py      |  15 +----
 4 files changed, 10 insertions(+), 227 deletions(-)

diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index 5492b6ba8..059354997 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -226,7 +226,7 @@ def plot_h12_calibration(
         else:
             return fig
 
-    def _h12_gwss_contig(
+    def _h12_gwss(
         self,
         contig,
         analysis,
@@ -279,39 +279,6 @@ def _h12_gwss_contig(
 
         return results
 
-    def _h12_gwss(
-        self,
-        contig,
-        analysis,
-        window_size,
-        sample_sets,
-        sample_query,
-        sample_query_options,
-        cohort_size,
-        min_cohort_size,
-        max_cohort_size,
-        random_seed,
-        chunks,
-        inline_array,
-    ):
-        results_tmp = self._h12_gwss_contig(
-            contig=contig,
-            analysis=analysis,
-            window_size=window_size,
-            sample_query=sample_query,
-            sample_sets=sample_sets,
-            sample_query_options=sample_query_options,
-            cohort_size=cohort_size,
-            min_cohort_size=min_cohort_size,
-            max_cohort_size=max_cohort_size,
-            random_seed=random_seed,
-            chunks=chunks,
-            inline_array=inline_array,
-        )
-        results = dict(x=results_tmp["x"], h12=results_tmp["h12"])
-
-        return results
-
     @check_types
     @doc(
         summary="Run h12 genome-wide selection scan.",
@@ -321,7 +288,7 @@ def _h12_gwss(
             contigs="An array with the contig for each window. The median is chosen for windows overlapping a change of contig.",
         ),
     )
-    def h12_gwss_contig(
+    def h12_gwss(
         self,
         contig: base_params.contig,
         window_size: h12_params.window_size,
@@ -364,9 +331,7 @@ def h12_gwss_contig(
             results = self.results_cache_get(name=name, params=params)
 
         except CacheMiss:
-            results = self._h12_gwss_contig(
-                chunks=chunks, inline_array=inline_array, **params
-            )
+            results = self._h12_gwss(chunks=chunks, inline_array=inline_array, **params)
             self.results_cache_set(name=name, params=params, results=results)
 
         x = results["x"]
@@ -375,65 +340,6 @@ def h12_gwss_contig(
 
         return x, h12, contigs
 
-    @check_types
-    @doc(
-        summary="Run h12 genome-wide selection scan.",
-        returns=dict(
-            x="An array containing the window centre point genomic positions.",
-            h12="An array with h12 statistic values for each window.",
-        ),
-    )
-    def h12_gwss(
-        self,
-        contig: base_params.contig,
-        window_size: h12_params.window_size,
-        analysis: hap_params.analysis = base_params.DEFAULT,
-        sample_query: Optional[base_params.sample_query] = None,
-        sample_query_options: Optional[base_params.sample_query_options] = None,
-        sample_sets: Optional[base_params.sample_sets] = None,
-        cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default,
-        min_cohort_size: Optional[
-            base_params.min_cohort_size
-        ] = h12_params.min_cohort_size_default,
-        max_cohort_size: Optional[
-            base_params.max_cohort_size
-        ] = h12_params.max_cohort_size_default,
-        random_seed: base_params.random_seed = 42,
-        chunks: base_params.chunks = base_params.native_chunks,
-        inline_array: base_params.inline_array = base_params.inline_array_default,
-    ) -> Tuple[np.ndarray, np.ndarray]:
-        # Change this name if you ever change the behaviour of this function, to
-        # invalidate any previously cached data.
-        name = "h12_gwss_v1"
-
-        params = dict(
-            contig=contig,
-            analysis=self._prep_phasing_analysis_param(analysis=analysis),
-            window_size=window_size,
-            sample_sets=self._prep_sample_sets_param(sample_sets=sample_sets),
-            # N.B., do not be tempted to convert this sample query into integer
-            # indices using _prep_sample_selection_params, because the indices
-            # are different in the haplotype data.
-            sample_query=sample_query,
-            sample_query_options=sample_query_options,
-            cohort_size=cohort_size,
-            min_cohort_size=min_cohort_size,
-            max_cohort_size=max_cohort_size,
-            random_seed=random_seed,
-        )
-
-        try:
-            results = self.results_cache_get(name=name, params=params)
-
-        except CacheMiss:
-            results = self._h12_gwss(chunks=chunks, inline_array=inline_array, **params)
-            self.results_cache_set(name=name, params=params, results=results)
-
-        x = results["x"]
-        h12 = results["h12"]
-
-        return x, h12
-
     @check_types
     @doc(
         summary="Plot h12 GWSS data.",
@@ -466,7 +372,7 @@ def plot_h12_gwss_track(
         inline_array: base_params.inline_array = base_params.inline_array_default,
     ) -> gplt_params.figure:
         # Compute H12.
-        x, h12, contigs = self.h12_gwss_contig(
+        x, h12, contigs = self.h12_gwss(
             contig=contig,
             analysis=analysis,
             window_size=window_size,
diff --git a/malariagen_data/anoph/h1x.py b/malariagen_data/anoph/h1x.py
index 1fcbd6b0a..8ee29d373 100644
--- a/malariagen_data/anoph/h1x.py
+++ b/malariagen_data/anoph/h1x.py
@@ -24,7 +24,7 @@ def __init__(
         # to the superclass constructor.
         super().__init__(**kwargs)
 
-    def _h1x_gwss_contig(
+    def _h1x_gwss(
         self,
         contig,
         analysis,
@@ -93,40 +93,6 @@ def _h1x_gwss_contig(
 
         return results
 
-    def _h1x_gwss(
-        self,
-        contig,
-        analysis,
-        window_size,
-        sample_sets,
-        cohort1_query,
-        cohort2_query,
-        cohort_size,
-        min_cohort_size,
-        max_cohort_size,
-        random_seed,
-        chunks,
-        inline_array,
-    ):
-        results_tmp = self._h1x_gwss_contig(
-            contig=contig,
-            analysis=analysis,
-            window_size=window_size,
-            cohort1_query=cohort1_query,
-            cohort2_query=cohort2_query,
-            sample_sets=sample_sets,
-            cohort_size=cohort_size,
-            min_cohort_size=min_cohort_size,
-            max_cohort_size=max_cohort_size,
-            random_seed=random_seed,
-            chunks=chunks,
-            inline_array=inline_array,
-        )
-
-        results = dict(x=results_tmp["x"], h1x=results_tmp["h1x"])
-
-        return results
-
     @check_types
     @doc(
         summary="""
@@ -139,7 +105,7 @@ def _h1x_gwss(
             contigs="An array with the contig for each window. The median is chosen for windows overlapping a change of contig.",
         ),
     )
-    def h1x_gwss_contig(
+    def h1x_gwss(
         self,
         contig: base_params.contig,
         window_size: h12_params.window_size,
@@ -182,9 +148,7 @@ def h1x_gwss_contig(
             results = self.results_cache_get(name=name, params=params)
 
         except CacheMiss:
-            results = self._h1x_gwss_contig(
-                chunks=chunks, inline_array=inline_array, **params
-            )
+            results = self._h1x_gwss(chunks=chunks, inline_array=inline_array, **params)
             self.results_cache_set(name=name, params=params, results=results)
 
         x = results["x"]
@@ -193,68 +157,6 @@ def h1x_gwss_contig(
 
         return x, h1x, contigs
 
-    @check_types
-    @doc(
-        summary="""
-            Run a H1X genome-wide scan to detect genome regions with
-            shared selective sweeps between two cohorts.
-        """,
-        returns=dict(
-            x="An array containing the window centre point genomic positions.",
-            h1x="An array with H1X statistic values for each window.",
-        ),
-    )
-    def h1x_gwss(
-        self,
-        contig: base_params.contig,
-        window_size: h12_params.window_size,
-        cohort1_query: base_params.sample_query,
-        cohort2_query: base_params.sample_query,
-        analysis: hap_params.analysis = base_params.DEFAULT,
-        sample_sets: Optional[base_params.sample_sets] = None,
-        cohort_size: Optional[base_params.cohort_size] = h12_params.cohort_size_default,
-        min_cohort_size: Optional[
-            base_params.min_cohort_size
-        ] = h12_params.min_cohort_size_default,
-        max_cohort_size: Optional[
-            base_params.max_cohort_size
-        ] = h12_params.max_cohort_size_default,
-        random_seed: base_params.random_seed = 42,
-        chunks: base_params.chunks = base_params.native_chunks,
-        inline_array: base_params.inline_array = base_params.inline_array_default,
-    ) -> Tuple[np.ndarray, np.ndarray]:
-        # Change this name if you ever change the behaviour of this function, to
-        # invalidate any previously cached data.
-        name = "h1x_gwss_v1"
-
-        params = dict(
-            contig=contig,
-            analysis=self._prep_phasing_analysis_param(analysis=analysis),
-            window_size=window_size,
-            # N.B., do not be tempted to convert these sample queries into integer
-            # indices using _prep_sample_selection_params, because the indices
-            # are different in the haplotype data.
-            cohort1_query=cohort1_query,
-            cohort2_query=cohort2_query,
-            sample_sets=self._prep_sample_sets_param(sample_sets=sample_sets),
-            cohort_size=cohort_size,
-            min_cohort_size=min_cohort_size,
-            max_cohort_size=max_cohort_size,
-            random_seed=random_seed,
-        )
-
-        try:
-            results = self.results_cache_get(name=name, params=params)
-
-        except CacheMiss:
-            results = self._h1x_gwss(chunks=chunks, inline_array=inline_array, **params)
-            self.results_cache_set(name=name, params=params, results=results)
-
-        x = results["x"]
-        h1x = results["h1x"]
-
-        return x, h1x
-
     @check_types
     @doc(
         summary="""
@@ -290,7 +192,7 @@ def plot_h1x_gwss_track(
         inline_array: base_params.inline_array = base_params.inline_array_default,
     ) -> gplt_params.figure:
         # Compute H1X.
-        x, h1x, contigs = self.h1x_gwss_contig(
+        x, h1x, contigs = self.h1x_gwss(
             contig=contig,
             analysis=analysis,
             window_size=window_size,
diff --git a/tests/anoph/test_h12.py b/tests/anoph/test_h12.py
index aa0b906a0..4a8e0db12 100644
--- a/tests/anoph/test_h12.py
+++ b/tests/anoph/test_h12.py
@@ -129,20 +129,8 @@ def test_h12_calibration(fixture, api: AnophelesH12Analysis):
 
 def check_h12_gwss(*, api, h12_params):
     # Run main gwss function under test.
-    x, h12 = api.h12_gwss(**h12_params)
 
-    # Check results.
-    assert isinstance(x, np.ndarray)
-    assert isinstance(h12, np.ndarray)
-    assert x.ndim == 1
-    assert h12.ndim == 1
-    assert x.shape == h12.shape
-    assert x.dtype.kind == "f"
-    assert h12.dtype.kind == "f"
-    assert np.all(h12 >= 0)
-    assert np.all(h12 <= 1)
-
-    x, h12, contigs = api.h12_gwss_contig(**h12_params)
+    x, h12, contigs = api.h12_gwss(**h12_params)
 
     # Check results.
     assert isinstance(x, np.ndarray)
diff --git a/tests/anoph/test_h1x.py b/tests/anoph/test_h1x.py
index 6cbb0df9e..b7b5362d6 100644
--- a/tests/anoph/test_h1x.py
+++ b/tests/anoph/test_h1x.py
@@ -110,20 +110,7 @@ def test_haplotype_joint_frequencies():
 
 def check_h1x_gwss(*, api, h1x_params):
     # Run main gwss function under test.
-    x, h1x = api.h1x_gwss(**h1x_params)
-
-    # Check results.
-    assert isinstance(x, np.ndarray)
-    assert isinstance(h1x, np.ndarray)
-    assert x.ndim == 1
-    assert h1x.ndim == 1
-    assert x.shape == h1x.shape
-    assert x.dtype.kind == "f"
-    assert h1x.dtype.kind == "f"
-    assert np.all(h1x >= 0)
-    assert np.all(h1x <= 1)
-
-    x, h1x, contigs = api.h1x_gwss_contig(**h1x_params)
+    x, h1x, contigs = api.h1x_gwss(**h1x_params)
 
     # Check results.
     assert isinstance(x, np.ndarray)

From b25acb2a482b920ec3877aa60769039e10acc483 Mon Sep 17 00:00:00 2001
From: jonbrenas <51911846+jonbrenas@users.noreply.github.com>
Date: Tue, 5 Nov 2024 15:48:04 +0000
Subject: [PATCH 33/33] Added some examples in the notebook.

---
 malariagen_data/anoph/gplt_params.py |  4 +-
 malariagen_data/anoph/h12.py         |  4 +-
 notebooks/plot_h12_h1x.ipynb         | 67 +++++++++++++++++++++++-----
 3 files changed, 61 insertions(+), 14 deletions(-)

diff --git a/malariagen_data/anoph/gplt_params.py b/malariagen_data/anoph/gplt_params.py
index 903a60267..838ff286c 100644
--- a/malariagen_data/anoph/gplt_params.py
+++ b/malariagen_data/anoph/gplt_params.py
@@ -1,7 +1,7 @@
 """Parameters for genome plotting functions. N.B., genome plots are always
 plotted with bokeh."""
 
-from typing import Literal, Mapping, Optional, Union, Final
+from typing import Literal, Mapping, Optional, Union, Final, Sequence
 
 import bokeh.models
 from typing_extensions import Annotated, TypeAlias
@@ -118,3 +118,5 @@
 ]
 
 contig_colors_default: Final[contig_colors] = list(bokeh.palettes.d3["Category20b"][5])
+
+colors: TypeAlias = Annotated[Sequence[str], "List of colors."]
diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
index b18c75703..8f1ccf730 100644
--- a/malariagen_data/anoph/h12.py
+++ b/malariagen_data/anoph/h12.py
@@ -587,7 +587,7 @@ def plot_h12_gwss_multi_overlay_track(
             )
 
         # Determine X axis range.
-        x, _ = res[list(cohort_queries.keys())[0]]
+        x, _, _ = res[list(cohort_queries.keys())[0]]
         x_min = x[0]
         x_max = x[-1]
         if x_range is None:
@@ -622,7 +622,7 @@ def plot_h12_gwss_multi_overlay_track(
         )
 
         # Plot H12.
-        for i, (cohort_label, (x, h12)) in enumerate(res.items()):
+        for i, (cohort_label, (x, h12, contig)) in enumerate(res.items()):
             fig.scatter(
                 x=x,
                 y=h12,
diff --git a/notebooks/plot_h12_h1x.ipynb b/notebooks/plot_h12_h1x.ipynb
index 3586907de..33e00f53a 100644
--- a/notebooks/plot_h12_h1x.ipynb
+++ b/notebooks/plot_h12_h1x.ipynb
@@ -75,7 +75,8 @@
     "coh2 = \"ML-2_Kati_gamb_2014\"\n",
     "coh1_query = f\"cohort_admin2_year == '{coh1}'\"\n",
     "coh2_query = f\"cohort_admin2_year == '{coh2}'\"\n",
-    "contig = \"2L\""
+    "contig = \"2L\"\n",
+    "contigs = \"2RL\""
    ]
   },
   {
@@ -114,6 +115,23 @@
     ")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4470d24c-8cf1-4d22-b774-0121b4560e27",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ag3.plot_h12_gwss(\n",
+    "    contig=contigs,\n",
+    "    analysis=\"gamb_colu\",\n",
+    "    window_size=2000,\n",
+    "    sample_query=coh1_query,\n",
+    "    sample_sets=\"3.0\",\n",
+    "    cohort_size=20,\n",
+    ")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -173,6 +191,25 @@
     ")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b4b7a8d2-95d0-48dc-a32f-3bc96aacfb9f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ag3.plot_h1x_gwss(\n",
+    "    contig=contigs,\n",
+    "    window_size=2000,\n",
+    "    cohort1_query=coh1_query,\n",
+    "    cohort2_query=coh2_query,\n",
+    "    sample_sets=\"3.0\",\n",
+    "    analysis=\"gamb_colu\",\n",
+    "    cohort_size=20,\n",
+    "    contig_colors=[\"red\", \"green\"]\n",
+    ")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -261,6 +298,22 @@
     "contig = \"2RL\""
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1aaa0573-723c-43b1-baea-750172c4dabc",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ffc7dc06-6bdb-42d2-a1fb-878612d10dd1",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -364,14 +417,6 @@
     "    cohort_size=20,\n",
     ")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "67e3bfcc",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -382,7 +427,7 @@
    "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m125"
   },
   "kernelspec": {
-   "display_name": "malariagen-data-python",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -396,7 +441,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.15"
+   "version": "3.10.11"
   },
   "vscode": {
    "interpreter": {