HoloNet.plotting.detect_pathway_related_genes

HoloNet.plotting.detect_pathway_related_genes(trained_MGC_model_list, lr_df, used_gene_list, X, adj, cell_type_names, pathway_oi, fname=None, xticks_position='bottom', figsize=None, linewidths=0.6)

Plotting Heatmaps for specific pathway related genes, and which ligand receptors affect these genes, and these FCEs come from which cell types.

Parameters

trained_MGC_model_list List[List[MGC_Model]]

A list of trained MGC model for generating the expression of one target gene.

lr_df DataFrame

The used preprocessed LR-gene dataframe, must contain the ‘LR_pair’ column.

used_gene_list List[str]

List of used target gene names.

X Tensor

The feature matrix used as the input of the trained_MGC_model_list.

adj Tensor

The adjacency matrix used as the input of the trained_MGC_model_list.

cell_type_names List[str]

List of cell-type names.

pathway_oi str

The pathway on interest. Should in the ‘pathway_name’ column of lr_df.

fname str | Path | NoneUnion[str, Path, None] (default: None)

The output file name. If None, not save the figure.

xticks_position default: 'bottom'

Plot xticks at ‘top’ or ‘bottom’.

figsize default: None

Set the figsize.

linewidths default: 0.6

Set the widths of inner lines of heatmap.

Return type

(DataFrame, DataFrame, DataFrame)

Returns

: Three dataframes for the three subplots.