pyVIA.plotting_via.get_gene_expression

pyVIA.plotting_via.get_gene_expression(via_object, gene_exp, cmap='jet', dpi=150, marker_genes=[], linewidth=2.0, n_splines=10, spline_order=4, fontsize_=8, marker_lineages=[], optional_title_text='', cmap_dict=None, conf_int=0.95, driver_genes=False, driver_lineage=None)[source]
Parameters:

  • via_object – via object

  • gene_exp (DataFrame) – dataframe where columns are features (gene) and rows are single cells

  • cmap (str) – default: ‘jet’

  • dpi (int) – default:150

  • marker_genes (list) – Default is to use all genes in gene_exp. other provide a list of marker genes that will be used from gene_exp.

  • linewidth (float) – default:2

  • n_slines – default:10 Note n_splines must be > spline_order.

  • spline_order (int) – default:4 n_splines must be > spline_order.

  • marker_lineages – Default is to use all lineage pathways. other provide a list of lineage number (terminal cluster number).

  • cmap_dict (dict) – {lineage number: ‘color’}

  • conf_int (float) – Confidence interval of gene expressions. Also used for identifying driver genes if driver_genes = True.

  • driver_genes (bool) – Set True to compute and plot top 3 upregulated & downregulated driver genes expressions given terminal cell fates.

  • driver_lineage (int) – Provide lineage used to compute driver genes if driver_genes=True.

Returns:

fig, axs