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.