This was a feature request from @sgfin that I am finally getting around to. The default is to compare each cluster to all other clusters.
Comparing to a particular cluster is useful if you want to compare two clusters of cells that are very similar (e.g. NK and T cells) or the same (e.g. two clusters of macrophages). This is exactly the case for Alexi/Grant's single-cell data where they want to compare one population of macrophages to another.
This was a feature request from @sgfin that I am finally getting around to. The default is to compare each cluster to all other clusters.
Comparing to a particular cluster is useful if you want to compare two clusters of cells that are very similar (e.g. NK and T cells) or the same (e.g. two clusters of macrophages). This is exactly the case for Alexi/Grant's single-cell data where they want to compare one population of macrophages to another.