stereo.plots.PlotCollection.marker_genes_scatter

PlotCollection.marker_genes_scatter(res_key, markers_num=10, genes=None, groups=None, values_to_plot=None, sort_by='scores', width=None, height=None)[source]

Scatter of marker genes

Parameters:

  • res_key (str) – results key, defaults to ‘marker_genes’.

  • markers_num (Optional[int]) – top N makers, defaults to 10.

  • genes (Optional[Sequence[str]]) – name of genes which would be shown on plot, markers_num is ignored if it is set, defaults to None.

  • groups (Optional[Sequence[str]]) – cell types which would be shown on plot, all cell types would be shown if set it to None, defaults to None.

  • values_to_plot (Optional[Literal['scores', 'logfoldchanges', 'pvalues', 'pvalues_adj', 'log10_pvalues', 'log10_pvalues_adj']]) – specify the value which color the plot, the mean expression in group would be set if set it to None defaults to None. available values include: [scores, logfoldchanges, pvalues, pvalues_adj, log10_pvalues, log10_pvalues_adj].

  • sort_by (Literal['scores', 'logfoldchanges', 'pvalues', 'pvalues_adj']) – specify the value which sort by when select top N markers, defaults to ‘scores’ available values include: [scores, logfoldchanges, pvalues, pvalues_adj].

  • out_path – the path to save the figure.

  • out_dpi – the dpi when the figure is saved.

  • width (Optional[int]) – the figure width in pixels.

  • height (Optional[int]) – the figure height in pixels.