problem when generating graphs about cellchat HOT 6 CLOSED

@yjlee0331 I feel sorry you have such issues. However, there is no issue when I tested the two cases you mentioned. For example, I can specify the vector by vertex.receiver = c(1,2,5,9,10,12). Can you re-install the package and restart the RStudio?

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@sqjin thank you so much for your response. The vertex.receiver works now (I didn't realize that cluster 0 actually should be "1"); however, I still have a problem with the graphs. Sometimes, if I reload the package, it works, but most of the time it doesn't work and I continue getting graphs like the one I showed above, even if I reinstall the package. The circle graph also looks like this:

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@yjlee0331 Not sure if this issue is due to the fact that the cluster index starts from 0. You might can re-name your cell clusters. If this still does not work, you can either share your CellChat object with me or ask your colleagues to test it.

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Any updates on this by chance? Having the exact same problem. Attempting to supply the factored labels to the object to replace them to see if it helps at all, I'm wondering if its an issue that comes from creating a cellchat object directly from a seurat object.

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@cswoboda When assigning new cell labels, you should use the addMeta and setIdent functions. Please check the last section in the tutorial on the interface with other tools.

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Thank you!

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