Marker subplots

This visualization function can be launched from class DigitalCellSorter at the stage of post-processing.

From submodule VisualizationFunctions:

class VisualizationFunctions(dataName='dataName', saveDir='', matplotlibMode='Agg', safePlotting=True, verbose=1)

Class of visualization functions for DigitalCellSorter

internalMakeMarkerSubplots(*args, **kwargs)

Produce subplots on each marker and its expression on all clusters

Parameters:

df: pandas.DataFrame

Data with marker genes expression

X_projection: 2d numpy.array

2D coordinates for each cell

hugo_cd_dict: dictionary

With aliases for hugo names of genes

NoFrameOnFigures: boolean, Default False

Whether to include frame on the figure

HideClusterLabels: boolean, Default False

Whether to print cluster labels on the figure

outlineClusters: boolean, Default True

Whether to outline the clusters with circles

analyzeBy: str, Default ‘cluster’

What level of lablels to include. Other possible option is ‘label’

Returns:

None

Usage:

Function used internally

DCS = DigitalCellSorter.DigitalCellSorter()

DCS.internalMakeMarkerSubplots(df_markers_expr, projection, hugo_cd_dict)

Example output: