sc_toolbox.plot.marker_dendrogram#

sc_toolbox.plot.marker_dendrogram(marker_table, threshold=0.7, column='cluster', log_fc_key='log_FC', label_size=10, orientation='top', figsize=(10, 4), save=None)[source]#

Plots a dendogram of used marker genes.

Parameters:

  • marker_table (DataFrame) – A marker table as generated by sct.calc.extended_marker_table

  • threshold (float) – Threshold for the log fold change

  • column (str) – Column to create pivot by; usually just the clusters

  • log_fc_key (str) – Key for the stored log fold changes in the marker table

  • label_size (int) – Font size of the labels

  • orientation (str) – Orientation of the figure; Currently just ‘top’ or no orientation

  • figsize (Tuple[int, int]) – Size of the figure as specified in matplotlib

  • save (Optional[str]) – Path to save the plot to

Example

../../_images/marker_dendrogram.png