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)[source]
- Parameters:
via_object – via object
gene_exp (
DataFrame
) – dataframe where columns are features (gene) and rows are single cellscmap (
str
) – default: ‘jet’dpi (
int
) – default:150marker_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:2n_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’}
- Returns:
fig, axs