metachat.pl.plot_LRC_markers

metachat.pl.plot_LRC_markers(adata, LRC_name, LRC_marker_genes, avg=False, figsize=(10, 5), plot_savepath=None)

Visualize expression of LRC (Long-Range Channel) marker genes in spatial omics data.

This function plots the spatial expression of selected LRC marker genes. It can either visualize individual genes separately or compute and plot the average expression of all selected markers.

Parameters

adataanndata.AnnData

Annotated data matrix with spatial coordinates stored in adata.obsm["spatial"].

LRC_namestr

Name tag for the LRC type (e.g., “CSF”, “Blood”). Used in plot titles and output naming.

LRC_marker_geneslist

List of LRC marker gene names to visualize. Genes not found in adata.var_names are automatically skipped.

avgbool, default=False

If True, plots the average expression of all marker genes. If False, plots each gene separately.

figsizetuple of float, default=(10, 5)

Figure size (width, height) in inches.

plot_savepathstr, optional

Path to save the figure (e.g. "results/LRC_markers_Blood.pdf"). If None, the figure is displayed interactively.

Returns

axmatplotlib.axes.Axes or list of Axes

Matplotlib axis or list of axes containing the rendered plot(s).

Notes

• Marker genes are filtered to retain only those present in adata.var_names.

• Average expression is computed directly from adata.X (converted to dense if needed).

• When multiple genes are plotted, they are arranged in a single row of subplots.