stereo.plots.PlotGenesInPseudotime.plot_genes_in_pseudotime

PlotGenesInPseudotime.plot_genes_in_pseudotime(marker_genes_res_key='marker_genes', group=None, sort_by='scores', topn=5, cmap='plasma', width=None, height=None, size=30, marker='.')[source]

Distribution of expression count of marker genes along with pseudotime

Parameters:

  • marker_genes_res_key (str) – Specifies the key to get result of find_marker_genes , defaults to ‘marker_genes’

  • group (Optional[str]) – Sepcifies the cell type to plot, defaults to None

  • sort_by (Literal['scores', 'pvalues', 'pvalues_adj', 'log2fc', 'pct', 'pct_rest']) – Get top N marker genes in this order, defaults to ‘scores’

  • topn (int) – Get top N marker genes, defaults to 5

  • cmap (str) – Color map, definded in matplotlib, defaults to ‘plasma’

  • width (Optional[int]) – The figure width in pixels, defaults to None

  • height (Optional[int]) – The figure height in pixels, defaults to None

  • size (int) – The size of markers in plot, defaults to 30

  • marker (str) – The style of markers in plot, defaults to ‘.’