c2v.pl.clones2cells

c2v.pl.clones2cells(adata, clones, obs_name=None, cells_color=None, clones_color=None, mode='highlite', cells_basis='X_umap', clones_basis='X_umap', keep_color=False, bg_color='lightgrey', selected_color='red', cells_cmap=None, clones_cmap=None, cells_palette=None, clones_palette=None, s_cells_bg=1, s_cells_selected=2, s_clones=6, width='auto', height=400, axes=False, norm_clones=None, norm_cells=None)

Draws two interactive sctterplots with gene expression (left) and clonal (right) embeddings. Selection on the right plot leads to the highliting (mode=’highlite’) or filtering (mode=’filter’) of cells from the corresponding clones. Selection on the left plot leads to coloring the right plot by the proportion of selected cells in clones.

Parameters:

adata sc.AnnData

Annotated data matrix with gene expression.

clones sc.AnnData

Annotated data matrix with clonal embeddings.

obs_name str, optional

Name of column in clones.obs with clone labels in gene expression AnnData. If not provided, will be taken from clones.uns[“obs_name”].

cells_color str, optional

Name of column in adata.obs with cells colors. If not provided, cells will be colored in bg_color.

clones_color str, optional

Name of column in clones.obs with clones colors. If not provided, clones will be colored in bg_color.

mode {"highlite", "filter"}, optional

Whether to highlite (mode=’highlite’) or filter (mode=’filter’) cells from the selected clones.

cells_basis str, optional

Name of key in adata.obsm with cells embeddings.

clones_basis str, optional

Name of key in clones.obsm with clonal embeddings.

keep_color bool, optional

Whether to keep color of cells in cells_color for mode=’highlite’.

bg_color str, optional

Color of unselected cells or clones.

selected_color str, optional

Color of selected cells if mode=’highlite’ and keep_color=False.

cells_cmap str, optional

Continuous color map for cells.

clones_cmap str, optional

Continuous color map for clones.

cells_palette str, optional

Palette (discrete colormap) for cells. If None, standard scanpy’s procedure for categorical coloring is used.

clones_palette str, optional

Palette (discrete colormap) for clones. If None, standard scanpy’s procedure for categorical coloring is used.

s_cells_bg int, optional

Size of unselected cells.

s_cells_selected int, optional

Size of selected cells.

s_clones int, optional

Size of clones.

width float, optional

Width of widget.

height float, optional

Height of widget.

axes bool, optional

Whether to show axes.

norm_clones tuple[float, float], optional

Range of values for clonal embeddings normalization.

norm_cells tuple[float, float], optional

Range of values for gene expression embeddings normalization.

Return type:

None

Returns:

None