Some cells do not show up on the outgoing but not on the incoming river plots.

[charlesgwellem]

Please is there a reason why a cell might appear when visualising the outgoing patterns but not the incoming patterns with river plots? In both cases I used the appropriate number of patterns from the cophenetic and silhouette plots i.e. for the outgoing pattern, the values drop sharply after pattern2 and after pattern 4 for the incoming.

I have highlighted one of my cells of interest which is present in the outgoing pattern but not in the incoming pattern.

[sqjin]

@charlesgwellem Can you check the associated heatmap plots? When generating river plot, a cutoff will be applied to simplify the connections. There is no cutoff in the heatmap plots. You can also modify the cutoff to see how it changes. If one cell group is not enriched in any pattern, it might be omitted in the river plot.