CellChat Two plots instead of one in Jupyter

Hi,

I'm using Jupyter lab to run the CellChat code. For some reason, the plots are duplicated, e.g. when I do this:

netVisual_diffInteraction(cellchat_combined, weight.scale = T)

I get the following output:

What could be the reason? Thanks in advance!

Mar 04 '25 09:03 f6v

@f6v Sorry. I just have no idea to use in Jupyter.

Mar 16 '25 08:03 sqjin

I also get duplicated plots when using netVisual_circle() in RStudio Quarto with Chunk Output Inline selected.

Mar 17 '25 10:03 AlbertoFabbri93

For me, this resolved when I would store the output of netVisual_xxx in a variable

ie gg <- netVisual_aggregate(cellChat, signaling = pathways.show, layout = "chord") instead of netVisual_aggregate(cellChat, signaling = pathways.show, layout = "chord")

Perhaps this is because the visualization functions are already plotting internally and also return the plot (hence are plotting twice if you don't store the output).

Oct 17 '25 02:10 dkzhang777