xchrom.pl.plot_motif_activity

xchrom.pl.plot_motif_activity(cell_embedding_ad: AnnData, celltype_key: str, tf_act_raw: AnnData, motif_name: str, save_path: str | None = None)[source]

Plot the activity of a single motif and celltype on UMAP.

Parameters:

  • cell_embedding_ad (anndata.AnnData) – Anndata object containing reduced dimension embedding

  • celltype_key (str) – Key for cell type in cell_embedding_ad.obs

  • tf_act_raw (anndata.AnnData) – Anndata object containing raw TF activity data

  • motif_name (str) – Name of the motif to plot

  • save_path (str, optional) – Path to save the plot

Return type:

None

Examples

>>> import xchrom as xc
>>> xc.pl.plot_motif_activity(
    cell_embedding_ad = covid19_rna,
    celltype_key = 'celltypeL0',
    tf_act_raw = tf_act,
    motif_name = 'RUNX3',
    save_path = './RUNX3_activity.pdf'
    )