NEW: adds pcoa plot

caporaso-lab · Oct 7, 2024 · e5aa087 · e5aa087
2 parents b9aa0ec + 900c1aa
commit e5aa087
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Showing 6 changed files with 650 additions and 78 deletions.
diff --git a/environments/gut-to-soil-manuscript-figures-qiime2-tiny-2024.5.yml b/environments/gut-to-soil-manuscript-figures-qiime2-tiny-2024.5.yml
@@ -1,16 +1,11 @@
 channels:
 - https://packages.qiime2.org/qiime2/2024.5/tiny/passed
+- https://packages.qiime2.org/qiime2/2024.5/amplicon/passed
 - conda-forge
 - bioconda
 dependencies:
   - qiime2-tiny
-  # Note 1: Add any additional conda dependencies here.
+  - q2-diversity
   - pip
   - pip:
-  # Note 2: Add any additional pip dependencies here.
-  #   - # some pip dependency
-  # Note 3: If you host your repository on GitHub, and you uncomment and modify
-  # the following lines to replace REPO-OWNER with the user or organization
-  # name that owns the repository, your installation commands can be updated to
-  # install from this file without additional steps.
-  #   - "gut-to-soil-manuscript-figures @ git+https://github.com/REPO-OWNER/gut-to-soil-manuscript-figures.git"
+    - gut_to_soil_manuscript_figures@git+https://github.com/caporaso-lab/gut-to-soil-manuscript-figures.git
diff --git a/gut_to_soil_manuscript_figures/_methods.py b/gut_to_soil_manuscript_figures/_methods.py
@@ -6,8 +6,80 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-import pandas as pd
+import os
+import pkg_resources
+import skbio
+import subprocess
 
+import qiime2
 
-def duplicate_table(table: pd.DataFrame) -> pd.DataFrame:
-    return table
+
+def pcoa_2d(output_dir: str, metadata: qiime2.Metadata,
+            ordination: skbio.OrdinationResults,
+            measure: str = 'Unweighted Unifrac',
+            average: bool = False, week_annotations: bool = False,
+            invert_x: bool = False, invert_y: bool = False,
+            swap_axes: bool = False, himalaya: bool = False,
+            pit_toilet: bool = False, export_legend: bool = False,
+            highlighted_buckets: str = ''):
+
+    md = metadata.to_dataframe()
+
+    metadata_fp = os.path.join(output_dir, 'metadata.tsv')
+    ordination_fp = os.path.join(output_dir, 'ordination.txt')
+
+    md.to_csv(metadata_fp, sep='\t', index_label='sample-id')
+    ordination.write(ordination_fp)
+
+    script_path = \
+        pkg_resources.resource_filename(
+            'gut_to_soil_manuscript_figures',
+            'scripts/plot_pcoa_2d.py'
+        )
+
+    average = str(average)
+    week_annotations = str(week_annotations)
+    invert_x = str(invert_x)
+    invert_y = str(invert_y)
+    swap_axes = str(swap_axes)
+    himalaya = str(himalaya)
+    pit_toilet = str(pit_toilet)
+    export_legend = str(export_legend)
+
+    plot_fp = os.path.join(output_dir, 'pcoa_plot.png')
+
+    if export_legend:
+        legend_fp = os.path.join(output_dir, 'legend.png')
+
+    command = [
+        'python', script_path,
+        metadata_fp,
+        ordination_fp,
+        measure,
+        average,
+        week_annotations,
+        plot_fp,
+        invert_x,
+        invert_y,
+        swap_axes,
+        himalaya,
+        pit_toilet,
+        export_legend,
+        highlighted_buckets,
+        legend_fp
+    ]
+    subprocess.run(command, check=True)
+
+    with open(os.path.join(output_dir, 'index.html'), 'w') as f:
+        f.write('''
+        <!DOCTYPE html>
+        <html>
+        <head>
+            <title>2D PCoA Plot</title>
+        </head>
+        <body>
+            <h1>2D PCoA Plot</h1>
+            <img src="pcoa_plot.png" alt="PCoA Plot">
+        </body>
+        </html>
+        ''')
diff --git a/gut_to_soil_manuscript_figures/plugin_setup.py b/gut_to_soil_manuscript_figures/plugin_setup.py
@@ -6,36 +6,41 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-from qiime2.plugin import Citations, Plugin
-from q2_types.feature_table import FeatureTable, Frequency
-from gut_to_soil_manuscript_figures import __version__
-from gut_to_soil_manuscript_figures._methods import duplicate_table
+from qiime2.plugin import Plugin, Metadata, Bool, Str
+
+from q2_types.ordination import PCoAResults
 
-citations = Citations.load("citations.bib", package="gut_to_soil_manuscript_figures")
+from gut_to_soil_manuscript_figures import __version__
+from gut_to_soil_manuscript_figures._methods import pcoa_2d
 
 plugin = Plugin(
-    name="gut-to-soil-manuscript-figures",
+    name='gut-to-soil-manuscript-figures',
     version=__version__,
-    website="https://github.com/caporaso-lab/gut-to-coil-manuscript-figures/",
-    package="gut_to_soil_manuscript_figures",
-    description="Plugin that contains methods for figure generation used in Jeff Meilander's PhD manuscript",
-    short_description="Plugin template.",
-    # The plugin-level citation of 'Caporaso-Bolyen-2024' is provided as
-    # an example. You can replace this with citations to other references
-    # in citations.bib.
-    citations=[citations['Caporaso-Bolyen-2024']]
+    website='https://github.com/caporaso-lab/gut-to-coil-manuscript-figures/',
+    package='gut_to_soil_manuscript_figures',
+    description="Plugin that contains methods for figure generation used in"
+                " Jeff Meilander's PhD manuscript.",
+    short_description=''
 )
 
-plugin.methods.register_function(
-    function=duplicate_table,
-    inputs={'table': FeatureTable[Frequency]},
-    parameters={},
-    outputs=[('new_table', FeatureTable[Frequency])],
-    input_descriptions={'table': 'The feature table to be duplicated.'},
+plugin.visualizers.register_function(
+    function=pcoa_2d,
+    inputs={'ordination': PCoAResults},
+    parameters={
+        'metadata': Metadata,
+        'measure': Str,
+        'average': Bool,
+        'week_annotations': Bool,
+        'invert_x': Bool,
+        'invert_y': Bool,
+        'swap_axes': Bool,
+        'himalaya': Bool,
+        'pit_toilet': Bool,
+        'export_legend': Bool,
+        'highlighted_buckets': Str
+    },
+    input_descriptions={},
     parameter_descriptions={},
-    output_descriptions={'new_table': 'The duplicated feature table.'},
-    name='Duplicate table',
-    description=("Create a copy of a feature table with a new uuid. "
-                 "This is for demonstration purposes only. 🧐"),
-    citations=[]
+    name='',
+    description=('')
 )