How to draw marker plots

As explained for fetal-liver example, it is possible to visualize selected genes.

For this, you need to provide a list of genes in a file or a single gene name. Just save how you run the workflow and rerun it with the same parameters.

You can visuzalize any gene after the workflow completes.

cellsnake standard data --resolution auto  -j 10

#or on an integrated dataset
cellsnake integrated standard analyses_integrated/seurat/integrated.rds --gene AHPS --resolution auto  -j 10

#it is also possible to give a file with a list of genes to visualize
cellsnake integrated standard analyses_integrated/seurat/integrated.rds --gene markers.tsv --resolution auto  -j 10