Significant interaction results between two cell types in df.net, but not in cellchat@net$count

[Chanele13]

Hi!

Could you please help me out with this problem:

I run the code "df.net <- subsetCommunication(cellchat, sources.use = c(35), targets.use = c(2))" and get the table attached to this post where there are some ligand-receptor interactions between my 2 sets of cells (35 and 2)

However, when I run this code "cellchat <- aggregateNet(cellchat, sources.use = c(35), targets.use=c(2), remove.isolate=F)" (with the same sources and targets as in the previous code), followed by this code "cellchat@net$count" this table gives me all 0 even for my cell type 35 and 2.

Why is that? Why do I not see any interactions?

Thanks!
Chanèle

[sqjin]

@Chanele13 There is no issue when I just tried it.

[Chanele13]

Hi @sqjin Thanks for your answer.

Do you meant that the number of interactions that you see in the table that you get from "df.net" is the same that you get in the table from the code "cellchat@net$count"? Because me I get just a list of 0 as shown in the picture attached here (where the set of cells 35 is "term_not" and the set of cells 2 is "alveolar macrophages".

Any idea why that would be? Thanks!