gene_expr_split_stacked

besca.pl.gene_expr_split_stacked(adata, genes, split_variable, label_split_variable=None, subset_variable='celltype', label_subset_variable=None, use_raw=True, fig_width=8, fig_height=4, order=None, inner='stick', figsize=(15, 8))[source]

Stacked violin plot for visualization of genes expression.

Parameters:

  • adata (AnnData) – The annotated data matrix used as input

  • genes (list) – List of gene ids for which the gene expression levels should be compared

  • split_variable (str) – string identfying the column which contains the annotation which cell belongs to which group (should only contain 2 different groups!!) If you have more than 2 groups you will need to look into other visualization techniques.

  • subset_variable (str) – string identifying the column along which the AnnData object should be split into subsets. Can contain as many groups as you wish. parameters

  • use_raw (bool (default = True)) – boolian indicator if adata.raw data should be used as input for gene expression levels

  • figsize ((width, height) or None | default = (15,8)) – optional parameter to define the figure size of the plot that is to be generated

  • order (lists of strings) – Order to plot the categorical levels in

  • inner (str (default = ‘stick’)) – see seaborn violin plot.

Return type:

fig