From 5d2c65eaedcea7a9bbb2a20b46404c0b25d6f065 Mon Sep 17 00:00:00 2001
From: Colin Wood <woodcolin38@gmail.com>
Date: Fri, 13 Sep 2024 15:14:20 -0700
Subject: [PATCH] filtered features visualizer

---
 q2_qsip2/plugin_setup.py             | 20 +++++++++++++++++++-
 q2_qsip2/visualizers/_visualizers.py | 18 ++++++++++++++++++
 2 files changed, 37 insertions(+), 1 deletion(-)

diff --git a/q2_qsip2/plugin_setup.py b/q2_qsip2/plugin_setup.py
index 050a19e..3dc0665 100644
--- a/q2_qsip2/plugin_setup.py
+++ b/q2_qsip2/plugin_setup.py
@@ -18,7 +18,7 @@
 )
 from q2_qsip2.visualizers._visualizers import (
     plot_weighted_average_densities, plot_sample_curves, plot_density_outliers,
-    show_comparison_groups
+    show_comparison_groups, plot_filtered_features
 )
 
 
@@ -231,4 +231,22 @@
     citations=[],
 )
 
+plugin.visualizers.register_function(
+    function=plot_filtered_features,
+    inputs={
+        'filtered_qsip_data': QSIP2Data[Filtered]
+    },
+    parameters={},
+    input_descriptions={
+        'filtered_qsip_data': 'Your filtered qsip data artifact.'
+    },
+    parameter_descriptions={},
+    name='Visualize feature retention.',
+    description=(
+        'Displays per-source stacked bar charts of feature retention by '
+        'relative abundance and feature count.'
+    ),
+    citations=[],
+)
+
 importlib.import_module('q2_qsip2.types._deferred_setup')
diff --git a/q2_qsip2/visualizers/_visualizers.py b/q2_qsip2/visualizers/_visualizers.py
index 2a09a1b..ab2e761 100644
--- a/q2_qsip2/visualizers/_visualizers.py
+++ b/q2_qsip2/visualizers/_visualizers.py
@@ -106,3 +106,21 @@ def show_comparison_groups(
         df = qsip2.show_comparison_groups(qsip_data, groups_vector)
 
     df.to_html(Path(output_dir) / 'index.html')
+
+
+def plot_filtered_features(output_dir: str, filtered_qsip_data: RS4) -> None:
+    '''
+    Displays per-source stacked bar charts showing the retention of features.
+
+    Parameters
+    ----------
+    output_dir : str
+        The root directory of the visualization loaded into the browser.
+    qsip_data : RS4
+        The "qsip_data" object.
+    '''
+    plot = qsip2.plot_filter_gradient_position(filtered_qsip_data)
+
+    _ggplot2_object_to_visualization(
+        plot, Path(output_dir), width=10, height=10
+    )