TrajAtlas.TRAVMap.plotGeneModule#
- TrajAtlas.TRAVMap.plotGeneModule(mdata, sample, factor, gene_num=20, **kwargs)[source]#
Plot the gene expression heatmap of the top genes within the selected gene module for the chosen sample.
See also
See Detect pseudotemporal gene modules with TRAVMap for how to detect pseudotemporal
gene modules.
- Parameters:
mdata (
MuData) – MuData object with pseudotemporal gene expression profile in MuData[‘tdiff’]uns[“cpm_dict”] and NMF factor in MuData[‘tdiff’]uns[“factor_dict”].sample (
str) – Selected sample (trajectory) to plot.interval_threshold – Minimal pseudotime interval number to check which sample to keep. (default: 30)
gene_threshold – Minimal gene number to check which sample to keep. (default: 1000)
n_factors – Number of NMF components. (default: ‘15’)
gene_num (
int) – Number of genes to plot.**kwargs – Keyword arguments for pch.ClusterMapPlotter.
factor (str) –
- Returns:
: Nothing. But plot gene expression heatmap.