Cell type markers pie plot

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

From submodule VisualizationFunctions:

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

Class of visualization functions for DigitalCellSorter

makeCellMarkersPiePlot(*args, **kwargs)

Make summary of markers comparison between two cell types.

Parameters:

type1: str

Name of the first cell type to compare

type2: str

Name of the second cell type to compare

df_marker_cell_type: pandas.DataFrame or str, Default ‘all’

Celltypes/Markers matrix. If ‘expressed’, then only expressed markers will be used. If ‘all’ then all markers of the input marker list will be used. If an instance of a pandas.DataFrame is passed, then its all markers will be used.

nameToAppend: str, Default None

String to append to the figure file name.

listUnexpressedMarkers: boolean, Default True

List (highlight) markers that are not expressed. This option is ignored unless df_marker_cell_type==’all’

orthogonalSectorsShift: float, Default 0.1

Sectors marked as ‘+/-’ and ‘-/+’ are shifted off-center. Set this parameter to zero to have round continuous pie chart.

rotationAngle: int or float, Default 0

Angle in degrees that will rotate the whole pie chart counterclockwise.

dpi: int, Default 600

Resolution of the figure image

extension: str, Default ‘png’

Format of the figure file

Returns:

Marker lists split into categories.

Usage:

DCS = DigitalCellSorter.DigitalCellSorter()

DCS.makeCellMarkersPiePlot(‘T cells’, ‘B cells’)

Example output: