density outlier visualizer

caporaso-lab · Sep 11, 2024 · b889cf5 · b889cf5
1 parent 66b817e
commit b889cf5
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Showing 2 changed files with 36 additions and 10 deletions.
diff --git a/q2_qsip2/plugin_setup.py b/q2_qsip2/plugin_setup.py
@@ -15,7 +15,7 @@
 from q2_qsip2.workflow import standard_workflow, create_qsip_data
 from q2_qsip2.types import QSIP2Data
 from q2_qsip2.visualizers._visualizers import (
-    plot_weighted_average_density, plot_sample_curves
+    plot_weighted_average_density, plot_sample_curves, plot_density_outliers
 )
 
 
@@ -100,13 +100,13 @@
 plugin.visualizers.register_function(
     function=plot_weighted_average_density,
     inputs={
-        'qsip_object': QSIP2Data
+        'qsip_data': QSIP2Data
     },
     parameters={
         'group': Str
     },
     input_descriptions={
-        'qsip_object': 'The qSIP data for which to plot the weighted average '
+        'qsip_data': 'The qSIP data for which to plot the weighted average '
                        'densities.'
     },
     parameter_descriptions={
@@ -121,15 +121,31 @@
 plugin.visualizers.register_function(
     function=plot_sample_curves,
     inputs={
-        'qsip_object': QSIP2Data
+        'qsip_data': QSIP2Data
     },
     parameters={},
     input_descriptions={
-        'qsip_object': 'The qSIP data for which to plot the per-sample density '
+        'qsip_data': 'The qSIP data for which to plot the per-source density '
                        'curves.'
     },
     parameter_descriptions={},
-    name='Plot per-sample density curves.',
+    name='Plot per-source density curves.',
+    description=('Placeholder'),
+    citations=[],
+)
+
+plugin.visualizers.register_function(
+    function=plot_density_outliers,
+    inputs={
+        'qsip_data': QSIP2Data
+    },
+    parameters={},
+    input_descriptions={
+        'qsip_data': 'The qSIP data for which to plot the per-source density '
+                       'outliers.'
+    },
+    parameter_descriptions={},
+    name='Plot per-source density outliers.',
     description=('Placeholder'),
     citations=[],
 )

diff --git a/q2_qsip2/visualizers/_visualizers.py b/q2_qsip2/visualizers/_visualizers.py
@@ -18,21 +18,31 @@
 qsip2 = importr('qSIP2')
 
 def plot_weighted_average_density(
-    output_dir: str, qsip_object: RS4, group: Optional[str] = None
+    output_dir: str, qsip_data: RS4, group: Optional[str] = None
 ) -> None:
     '''
     '''
-    plot = qsip2.plot_source_wads(qsip_object, group=group)
+    plot = qsip2.plot_source_wads(qsip_data, group=group)
 
     _ggplot2_object_to_visualization(
         plot, Path(output_dir), width=10, height=4
     )
 
 
-def plot_sample_curves(output_dir: str, qsip_object: RS4) -> None:
+def plot_sample_curves(output_dir: str, qsip_data: RS4) -> None:
     '''
     '''
-    plot = qsip2.plot_sample_curves(qsip_object)
+    plot = qsip2.plot_sample_curves(qsip_data)
+
+    _ggplot2_object_to_visualization(
+        plot, Path(output_dir), width=10, height=10
+    )
+
+
+def plot_density_outliers(output_dir: str, qsip_data: RS4) -> None:
+    '''
+    '''
+    plot = qsip2.plot_density_outliers(qsip_data)
 
     _ggplot2_object_to_visualization(
         plot, Path(output_dir), width=10, height=10