stereo.plots.PlotCollection.umap#
- PlotCollection.umap(gene_names=None, res_key='umap', cluster_key=None, title=None, x_label='umap1', y_label='umap2', dot_size=None, colors='stereo', width=None, height=None, palette=None, vmin=None, vmax=None, **kwargs)[source]#
Scatter plot of UMAP after reducing dimensionalities.
- Parameters:
gene_names (
Union
[ndarray
,list
,str
,None
]) – the list of gene names.cluster_key (
Optional
[str
]) – the result key of clustering.res_key (
str
) – the result key of UMAP.title (
Union
[str
,list
,None
]) – the plot title.x_label (
Union
[str
,list
,None
]) – the x label.y_label (
Union
[str
,list
,None
]) – the y label.dot_size (
Optional
[int
]) – the dot size.colors (
Union
[str
,list
,None
]) – the color list.width (
Optional
[int
]) – the figure width in pixels.height (
Optional
[int
]) – the figure height in pixels.palette (
Optional
[int
]) – color theme.out_path – the path to save the figure.
out_dpi – the dpi when the figure is saved.
vmin (
Optional
[float
]) – The value representing the lower limit of the color scale. Values smaller than vmin are plotted with the same color as vmin.vmax (
Optional
[float
]) – The value representing the lower limit of the color scale. Values smaller than vmin are plotted with the same color as vmin.