nichesphere.coloc.spatialSingleCTPlot

nichesphere.coloc.spatialSingleCTPlot(adata, cell_type, CTprobs, spot_size=1, legend_fontsize=7, title='', legend_loc='right margin', save_name='test.pdf', ax=None, vmin=0, vmax=None, cmap='magma')

Plot a single cell type proportions in spatial data (MERFISH / visium slices)

Parameters:

• adata (AnnData) – sample specific spatial anndata object

• CTprobs (pd.DataFrame (default: None)) – sample specific cell type probabilities per spot (not needed if there is a cell type column (maxCT_col) in the anndata obs)

• cell_type (str) – cell type to plot

• spot_size (int (default: 1)) – size of spots in the spatial plot

• legend_fontsize (int (default: 7))

• title (str)

• legend_loc (str (default: 'right margin')) – legend location , can switch to ‘on data’

• save_name (str (default: 'test.pdf'))

• ax (matplotlib.axes.Axes (default: None)) – The axes object to draw the plot onto.

• vmin (int (default: 0)) – Minimum value in the color scale

• vmax (int (default: None)) – Maximum value in the color scale

• cmap (str (default: 'magma')) – Name of the color map to be used

Return type:

Spatial plot where spots are colored by probability of the selected cell type