commot.pl.plot_communication_dependent_genes

commot.pl.plot_communication_dependent_genes(df_deg, df_yhat, show_gene_names=True, top_ngene_per_cluster=- 1, colormap='magma', cluster_colormap='Plotly', font_scale=1.4, filename=None, return_genes=False)

Plot smoothed gene expression of the detected communication-dependent genes. Takes input from tl.communication_deg_clustering.

../_images/communication_deg.png
Parameters
  • df_deg (DataFrame) – A data frame where each row is a gene and the columns should include ‘waldStat’, ‘pvalue’, ‘cluster’. Output of tl.communication_deg_clustering

  • df_yhat (DataFrame) – A data frame where each row is the smoothed expression of a gene. Output of tl.communication_deg_clustering.

  • show_gene_names (bool) – Whether to plot the gene names.

  • top_ngene_per_cluster (int) – If non-negative, plot the top_ngene_per_cluster genes with highest wald statistics.

  • colormap (str) – The colormap for the heatmap. Choose from available colormaps from seaborn.

  • cluster_colormap (str) – The qualitative colormap for annotating gene cluster labels. Choose from ‘Plotly’, ‘Alphabet’, ‘Light24’, ‘Dark24’.

  • font_scale (float) – Font size.

  • filename – Filename for saving the figure. Set the name to end with ‘.pdf’ or ‘png’ to specify format.

  • return_genes – Whether to return the list of plotted genes.

Returns

Returns the gene list being plotted if return_genes is True.

Return type

genes