Question : plot_genes_in_pseudotime / Module

cole-trapnell-lab / monocle3

Other

327 stars 101 forks source link

Question : plot_genes_in_pseudotime / Module #463

Open KatsuyukiNAKANISHI opened 3 years ago

KatsuyukiNAKANISHI commented 3 years ago

Dear all,

I'd like to find upregulated / downregulated genes over trajectory. Is there any way to make a graph of plot_genes_in_pseudotime() for Module? I want to know how each modules changes over a trajectory.

Best,

Katsu

brgew commented 3 years ago

Hi,

I believe that you can subset the cds by the genes in your gene module and pass that subset to plot_genes_pseudotime(). Does this answer your question?

lb15 commented 3 years ago

Hi, I have the same question. Some of my modules have greater than 100 genes, so I get an error with plot_gene_pseudotime() about needing to subset the cds first. In general, is there a way to get the module expression score values (either raw or scaled to min-max) for each cell to do some manual plotting against other factors? Thanks!