COSIE.downstream_analysis.highlight_joint_clusters_all_sections

highlight_joint_clusters_all_sections(cluster_labels, data_dict, n_clusters, highlight_labels, vis_basis='spatial', colormap=None, swap_xy=False, invert_x=False, invert_y=False, offset=False, save_dir=None, figscale=35, dpi=300, remove_title=True, remove_legend=True, remove_spine=True, bg_color=[200, 200, 200])

Visualize and highlight specified clusters across all tissue sections. For each section, this function renders a spatial plot of cell clusters, highlighting the clusters specified in highlight_labels using distinct colors, while rendering all other clusters in a uniform background color.

Parameters

cluster_labelsdict

Dictionary of {section_id: np.ndarray of cluster labels} for each section.

data_dictdict

Dictionary of input data.

n_clustersint

Total number of clusters.

highlight_labelslist of int

List of cluster labels to highlight. Other clusters are rendered with background color.

vis_basisstr, default “spatial”

Key in obsm specifying the coordinate basis to use.

colormapstr or list or None, default None

Name of matplotlib colormap to use, or a list of RGB values. If None, uses a default palette.

swap_xybool, default False

Whether to swap x and y axes in the coordinate system.

invert_xbool, default False

Whether to flip the image horizontally.

invert_ybool, default False

Whether to flip the image vertically.

offsetbool, default False

Whether to shift coordinates to (0, 0) minimum before rendering.

save_dirstr or None, default None

If provided, saves each figure as a JPEG to the specified directory.

figscalefloat, default 35

Controls the scaling of the figure size.

dpiint, default 300

Resolution of the saved figure.

remove_titlebool, default True

Whether to remove the figure title.

remove_legendbool, default True

Whether to remove the cluster legend from the plot.

remove_spinebool, default True

Whether to remove the axis spines (borders around the plot).

bg_colorlist of int, default [200, 200, 200]

RGB color used for non-highlighted clusters.

Returns

None