Merge branch 'CW-4904' into 'dev'

Path for SeqCompare to work with Bokeh plots [CW-4904]

Closes CW-4904

See merge request epi2melabs/ezcharts!199

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed 
 - Transparent lines/points plotted in relational plots.
 - Add `hover` back to bokeh toolbox.
+- `SeqCompare` not working with histograms and line charts from `BokehPlots`.
 ### Removed
 - BcftoolsStats component until it is updated to use BokehPlot.
 

ezcharts/components/fastcat.py

@@ -14,6 +14,7 @@
 from ezcharts.components.reports.comp import ComponentReport
 from ezcharts.layout.base import Snippet
 from ezcharts.layout.snippets import DataTable, Grid, Tabs
+from ezcharts.plots import BokehPlot
 
 
 FASTCAT_COLS_DTYPES = {
@@ -484,31 +485,51 @@ def _is_empty_plot(self, plot):
         """Check if the plot is empty."""
         if not plot:
             return True
-        if not plot.dataset:
-            return True
+        if isinstance(plot, BokehPlot):
+            if "_fig" not in dir(plot):
+                return True
+            for renderer in plot._fig.renderers:
+                if not hasattr(renderer, 'glyph'):
+                    return True
+        else:
+            if not plot.dataset:
+                return True
         return False
 
     def _coordinate_plots(self, plots, labels=None):
         """Coordinate the axes between the plots."""
         max_by_plot = []
         for plot in plots:
             if not self._is_empty_plot(plot):
-                dimensions = np.array(plot.dataset[0].dimensions)
-                if 'y' in dimensions:
-                    y_col = np.where(dimensions == 'y')[0]
+                if isinstance(plot, BokehPlot):
+                    dimensions = plot._fig.renderers[0].data_source.to_df()
+                    if 'top' in dimensions.columns:
+                        col = 'top'
+                    else:
+                        col = 'y'
+                    y_val = dimensions[col].max()
                 else:
-                    y_col = np.where(dimensions == 'height')[0]
-                max_by_plot.append(np.max(plot.dataset[0].source, axis=0)[y_col])
+                    dimensions = np.array(plot.dataset[0].dimensions)
+                    if 'y' in dimensions:
+                        y_col = np.where(dimensions == 'y')[0]
+                    else:
+                        y_col = np.where(dimensions == 'height')[0]
+                    y_val = np.max(plot.dataset[0].source, axis=0)[y_col]
+                max_by_plot.append(y_val)
         # Set new values
         if labels:
             inputs = zip(plots, labels)
         else:
             inputs = zip(plots, [None] * len(plots))
         for (plot, label) in inputs:
             if not self._is_empty_plot(plot):
-                plot.yAxis.max = max(max_by_plot)
-            if label:
-                plot.title.text = label
+                plot._fig.y_range.end = max(max_by_plot)
+                if label:
+                    plot._fig.add_layout(
+                        Title(text=label, text_font_size="1.5em"), 'above')
+            else:
+                if label:
+                    plot.title.text = label
 
     def _draw_bamstat_table(self, data):
         if not isinstance(data, pd.DataFrame):

ezcharts/data/test/histogram_stats/sample_2/length.hist

@@ -405,10 +405,10 @@
 701	702	8
 702	703	8
 703	704	6
-704	705	9
-705	706	13
+704	705	19
+705	706	23
 706	707	9
-707	708	11
+707	708	21
 708	709	6
 709	710	5
 710	711	5

ezcharts/data/test/histogram_stats/sample_2/quality.hist

@@ -120,9 +120,9 @@
 11.60	11.62	6
 11.62	11.64	17
 11.64	11.66	7
-11.66	11.68	16
-11.68	11.70	11
-11.70	11.72	6
+11.66	11.68	26
+11.68	11.70	21
+11.70	11.72	16
 11.72	11.74	8
 11.74	11.76	9
 11.76	11.78	10

ezcharts/demo.py

@@ -14,7 +14,7 @@
 from ezcharts.components.dss import load_dml, load_dmr
 from ezcharts.components.ezchart import EZChart
 from ezcharts.components.fastcat import load_bamstats_flagstat, load_stats
-from ezcharts.components.fastcat import SeqSummary
+from ezcharts.components.fastcat import SeqCompare, SeqSummary
 from ezcharts.components.modkit import load_bedmethyl, load_modkit_summary
 from ezcharts.components.mosdepth import load_mosdepth_regions, load_mosdepth_summary
 from ezcharts.components.nextclade import NextClade, NXTComponent
@@ -164,6 +164,13 @@ def example_plot(style="line") -> Plot:
             seq_summary=histogram_stats_dir,
             color="#2a98b7",
             sample_names=tuple(['sample_1', 'sample_2', 'sample_3']))
+    with report.add_section('Compare Summaries', 'Compare'):
+        SeqCompare(
+            histogram_stats_dir,
+            sample_names=tuple(['sample_1', 'sample_2', 'sample_3']),
+            alignment_stats=False,
+            color="#2a98b7",
+        )
 
     # This also adds to main_content, but provides a nice
     # container snippet as a starting context.