update

ChangeLog.md

@@ -1,3 +1,6 @@
+- 1.3.7.2
+   * Added documentation of the function makeViolinPlot
+
 - 1.3.7.1
    * Added makeViolinPlot visualization function enabling exploratory analysis of the numeric values distributions for comparison between categorical variables
 

docs/source/VisualizationFunctions.rst

@@ -26,6 +26,7 @@ at the stage of post-processing.
    visFunctions/makeMarkerExpressionPlot
    visFunctions/makeTtestPlot
    visFunctions/makePlotOfNewMarkers
+   visFunctions/makeViolinPlot
 
 
 

docs/source/visFunctions/makeViolinPlot.rst

@@ -0,0 +1,43 @@
+**Customized violin plot**
+==========================
+
+This visualization function can be launched from `class DigitalCellSorter`.
+By default the function also exports a summary of the data.
+
+From submodule `VisualizationFunctions`: 
+
+
+.. autoclass:: DigitalCellSorter.VisualizationFunctions.VisualizationFunctions
+    :noindex:
+
+    .. automethod:: makeViolinPlot
+
+
+**Example with synthetic data:**
+
+.. code-block:: python
+
+    data = pd.DataFrame({'Celltype': np.where((np.random.rand(1000)>0.7), 'Epithelial', 'Endothelial'), 
+                         'Condition': np.random.rand(1000)>0.3, 
+                         'Gene 1': np.log(np.random.rand(1000)*3 + 1), 
+                         'Gene 2': np.log(np.random.rand(1000)*1.5 + 1)})
+
+    DCS = DigitalCellSorter.DigitalCellSorter()
+    DCS.makeViolinPlot(data, ['Gene 1', 'Gene 2'], 
+                       dimPanels='Celltype', dimCategories='Condition', 
+                       title='{name}: {gene}', ylabel='Condition',
+                       pointsSize=5, fontsize=12)
+
+
+**Example output:**
+
+.. thumbnail:: https://github.com/sdomanskyi/DigitalCellSorter/blob/master/docs/examples/output/violin_plot.png?raw=true
+    :title: Example
+    :alt: Cannot load this figure
+    :align: center
+    :width: 250px
+    :height: 250px
+    :download: false
+
+
+

setup.py

@@ -12,7 +12,7 @@
 setup(
     name='DigitalCellSorter',
     packages=find_packages(),
-    version='1.3.7.1',
+    version='1.3.7.2',
     description='Toolkit for analysis and identification of cell types from heterogeneous single cell RNA-seq data',
     long_description_content_type="text/markdown",
     long_description=long_description,