compare two group interaction and sigficant pathway

[hansong798]

Hi, thank you for your advanced tool, cellchat team!

I have a question about relative information flow bar plot like below.
When compared two group with running below code, I got the bar plot and result with p value.
rankNet(cellchat.merged, comparison = c(1, 2),mode = "comparison", stacked = T, color.use=c('#969696','#E2AE33'), return.data = T,do.stat = TRUE)

And from #123 , I have understood that pathways that have significant difference for each dataset have each dataset color and pathways that are equally important in both the datasets is in black.

However, as you see below, "MPZ","ESAM","CD96","NECTIN" pathways are in black although it has low pvalue considering 0.05 threshold.

Did I understand wrong way?

[sqjin]

@hansong798 Here is because you have a relative contribution being 1.0. Please check the parameter tol = 0.05. If the relative change is small, we consider it as no change. Both criteria should be satisfied.