Add EMPress plot (#20)

* Add EMPress support

* update readme

* update rulegraph with empress

* update songbird env

* add iow to songbird

* add bioconda channel to songbird env

README.md

@@ -25,6 +25,11 @@ You should also change the model covariate, target, and reference category.
 
 If you have other confounders, you can include them under the `confounders` heading.
 Delete these if you are not including any additional confounders.
+Note you should still leave the `counfounders` entry - just delete the entries in the list.
+
+Qadabra can also output an [EMPress plot](https://journals.asm.org/doi/10.1128/mSystems.01216-20) of a phylogenetic tree annotated with each tool's differentials.
+Change the `tree` entry to point to this file.
+If you do not have a phylogenetic tree, change this entry to an empty string and EMPress will not be run.
 
 Run `snakemake --use-conda <other options>` to start the workflow.
 Please read the [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/executing/cli.html) for how to run Snakemake best on your system.

config/config.yaml

@@ -1,5 +1,6 @@
 table: "data/table.biom"
 metadata: "data/metadata.tsv"
+tree: "data/tree.nwk"
 stylesheet: "config/qadabra.mplstyle"
 model:
     covariate: anemia

workflow/Snakefile

@@ -5,6 +5,7 @@ include: "rules/common.smk"
 include: "rules/diffab.smk"
 include: "rules/visualization.smk"
 include: "rules/ml.smk"
+include: "rules/tree.smk"
 
 
 report: "report/workflow.rst"

workflow/envs/qadabra-songbird.yaml

@@ -1,6 +1,13 @@
-channel:
+channels:
     - conda-forge
+    - bioconda
 dependencies:
+    - iow
+    - cython
     - songbird
     - pandas>=0.18.0,<1
     - qurro
+    - pip
+    - pip:
+        - empress
+

workflow/report/empress.rst

@@ -0,0 +1 @@
+EMPress plot of phylogenetic tree. Tool differentials are included as feature metadata. For more information on EMPress, see `Cantrell and Fedarko et al., 2021 <https://journals.asm.org/doi/10.1128/mSystems.01216-20>`_.

workflow/report/qurro.rst

@@ -1 +1 @@
-Qurro visualization of differentials from all tools. For more information on Qurro, see `Fedarko 2020 <https://academic.oup.com/nargab/article/2/2/lqaa023/5826153>`_.
+Qurro visualization of differentials from all tools. For more information on Qurro, see `Fedarko et al., 2020 <https://academic.oup.com/nargab/article/2/2/lqaa023/5826153>`_.

workflow/rules/common.smk

@@ -34,9 +34,13 @@ all_viz_files.extend(
 all_viz_files.append("figures/rank_comparisons.html")
 all_viz_files.append("figures/pca.svg")
 
+if config["tree"]:
+    all_viz_files.append("results/empress")
+
 all_input = all_viz_files.copy()
 all_input.extend(["results/qurro", "results/differentials_table.html"])
 
+
 covariate = config["model"]["covariate"]
 reference = config["model"]["reference"]
 target = config["model"]["target"]

workflow/rules/visualization.smk

@@ -195,3 +195,27 @@ rule create_table:
         "../envs/qadabra-default.yaml"
     script:
         "../scripts/create_table.py"
+
+
+rule empress:
+    input:
+        tree=config["tree"],
+        diff="results/concatenated_differentials.tsv",
+    output:
+        report(
+            directory("results/empress"),
+            caption="../report/empress.rst",
+            htmlindex="empress.html",
+            category="Tree",
+        ),
+    log:
+        "log/empress.log",
+    conda:
+        "../envs/qadabra-songbird.yaml"
+    shell:
+        """
+        empress tree-plot \
+            --tree {input.tree} \
+            --feature-metadata {input.diff} \
+            --output-dir {output} > {log} 2>&1
+        """