Hello,
I have simply ran scanpy.tl.rank_genes_groups(). After obtaining the results per cluster with scanpy.get.rank_genes_groups_df(), I filter them using a pval threshold of 0.05 and a lfc threshold of 1.
Unfortunatly, for one of the cluster the lfc were mostly negative. To get around this problem, I have used absolute value for the lfc, which works fine.
Nevertheless, when using the scanpy.pl.dotplot(), the cluster where lfc were mostly negative shows basicaly nothing.
I guess that it is because this function doesn’t take into account downregulation of genes, thus I want to know if there is a way to efficiently show downregulated genes in dot plot ?
Thanks in advance !