support custom colors in plots

q2_micom/_viz.py

@@ -7,12 +7,12 @@
 from qiime2 import MetadataColumn
 
 
-def plot_growth(output_dir: str, results: GrowthResults) -> None:
+def plot_growth(
+    output_dir: str, results: GrowthResults, metadata: MetadataColumn = None
+) -> None:
     """Plot the taxa growth rates."""
-    viz.plot_growth(
-        results,
-        join(output_dir, "index.html"),
-    )
+    meta = None if metadata is None else metadata.to_series()
+    viz.plot_growth(results, join(output_dir, "index.html"), groups=meta)
 
 
 def exchanges_per_sample(
@@ -31,13 +31,16 @@ def exchanges_per_taxon(
     output_dir: str,
     results: GrowthResults,
     direction: str = "import",
+    metadata: MetadataColumn = None,
     perplexity: int = 20,
 ) -> None:
     """Plot the exchange fluxes."""
+    meta = None if metadata is None else metadata.to_series()
     viz.plot_exchanges_per_taxon(
         results,
         join(output_dir, "index.html"),
         direction,
+        groups=meta,
         perplexity=perplexity,
     )
 

q2_micom/plugin_setup.py

@@ -400,14 +400,14 @@
 plugin.visualizers.register_function(
     function=q2_micom.plot_growth,
     inputs={"results": MicomResults},
-    parameters={},
+    parameters={"metadata": MetadataColumn[Categorical]},
     input_descriptions={
         "results": (
             "A set of MICOM analysis results. "
             "Contains predicted groath rates and exchange fluxes."
         )
     },
-    parameter_descriptions={},
+    parameter_descriptions={"metadata": "The metadata variable to use."},
     name="Plot taxa growth rates.",
     description=(
         "Plot predicted growth rates for each taxon in each sample. "
@@ -451,6 +451,7 @@
     inputs={"results": MicomResults},
     parameters={
         "direction": Str % Choices("import", "export"),
+        "metadata": MetadataColumn[Categorical],
         "perplexity": Int % Range(2, None),
     },
     input_descriptions={
@@ -461,6 +462,7 @@
     },
     parameter_descriptions={
         "direction": "The direction of the flux.",
+        "metadata": "The metadata variable to use.",
         "perplexity": "TSNE parameter. Relates to the number of neighbors used to "
         "calculate distances. Smaller values preserve more local "
         "structure and larger values preserve more global structure.",

q2_micom/tests/test_viz.py

@@ -14,9 +14,14 @@
 
 def test_growth_plots():
     r = results.view(GrowthResults)
+    mcol = q2.Metadata.load(path.join(this_dir, "data", "metadata.tsv")).get_column(
+        "status"
+    )
     with TemporaryDirectory(prefix="q2-micom-") as d:
         q2m.plot_growth(str(d), r)
         assert q2m.tests.check_viz(str(d))
+        q2m.plot_growth(str(d), r, metadata=mcol)
+        assert q2m.tests.check_viz(str(d))
 
 
 def test_exchanges_per_sample():
@@ -28,9 +33,14 @@ def test_exchanges_per_sample():
 
 def test_exchanges_per_taxon():
     r = results.view(GrowthResults)
+    mcol = q2.Metadata.load(path.join(this_dir, "data", "metadata.tsv")).get_column(
+        "status"
+    )
     with TemporaryDirectory(prefix="q2-micom-") as d:
         q2m.exchanges_per_taxon(str(d), r)
         assert q2m.tests.check_viz(str(d))
+        q2m.exchanges_per_taxon(str(d), r, metadata=mcol)
+        assert q2m.tests.check_viz(str(d))
 
 
 def test_plot_tradeoff():

setup.cfg

@@ -12,7 +12,7 @@ long_description = file: README.md
 long_description_content_type = text/markdown
 license = Apache License 2.0
 url = https://github.com/micom-dev/q2-micom
-classifiers = 
+classifiers =
 	Development Status :: 4 - Beta
 	Intended Audience :: Science/Research
 	Topic :: Scientific/Engineering :: Bio-Informatics
@@ -22,7 +22,7 @@ classifiers =
 	Programming Language :: Python :: 3.9
 	Programming Language :: Python :: 3.10
 	Programming Language :: Python :: 3.11
-keywords = 
+keywords =
 	microbiome
 	modeling
 	metabolism
@@ -32,26 +32,26 @@ keywords =
 zip_safe = False
 packages = find:
 python_requires = >=3.6
-install_requires = 
+install_requires =
 	cobra>=0.29.0
-	micom>=0.36.0
+	micom>=0.37.0
 	jinja2>=2.10.3
 	qiime2>=2023.2
 	rich>=6.0
 	pandas>=1.0
 	numpy<2.0
-tests_require = 
+tests_require =
 	coverage
 	pytest
 	pytest-cov
 	flake8
 
 [options.package_data]
-q2_micom = 
+q2_micom =
 	citations.bib
 
 [options.entry_points]
-qiime2.plugins = 
+qiime2.plugins =
 	q2-micom = q2_micom.plugin_setup:plugin
 
 [bumpversion:file:setup.py]
@@ -63,7 +63,7 @@ search = __version__ = "{current_version}"
 replace = __version__ = "{new_version}"
 
 [tool:pytest]
-filterwarnings = 
+filterwarnings =
 	ignore::DeprecationWarning
 	ignore::FutureWarning
 
@@ -76,15 +76,15 @@ branch = True
 omit = q2_micom/tests/*
 
 [coverage:report]
-exclude_lines = 
+exclude_lines =
 	pragma: no cover
-	
+
 	def __repr__
 	if self\.debug
-	
+
 	raise AssertionError
 	raise NotImplementedError
-	
+
 	if 0:
 	if __name__ == .__main__.:
 ignore_errors = True