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sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
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netMappingDEG error #698

Open vasikara17 opened 1 year ago

vasikara17 commented 1 year ago

Hello, thank you for a really useful tool! I wanted to do a comparison and between my two conditions. I am using the part your vignette: Identify dysfunctional signaling by using differential expression analysis Here is the code and the error: cellchat <- identifyOverExpressedGenes(cellchat, group.dataset = "sample", pos.dataset = pos.dataset, features.name = features.name, only.pos = FALSE, thresh.pc = 0.1, thresh.fc = 0.1, thresh.p = 1) net <- netMappingDEG(cellchat,features.name = features.name) net <- netMappingDEG(cellchat,features.name = features.name) Error in [[<-.data.frame(*tmp*, ii, value = list(11L, 11L, 11L, 11L, : replacement has 1330 rows, data has 1329 I cannot identify where this is coming from. I would appreciate your feedback on that. Thank you in advance

kaizen89 commented 10 months ago

I have the exact same error

net = netMappingDEG(cellchat, features.name = "features",thresh = 0.05)
Error in `[[<-.data.frame`(`*tmp*`, ii, value = list(1L, 2L, 3L, 4L, 5L,  : 
  replacement has 5167 rows, data has 5166
sqjin commented 10 months ago

@kaizen89 If you can share a cellchat object that can replicate your error, then I can test it.

kaizen89 commented 10 months ago

@sqjin sure. Here's the object: link Thanks

sqjin commented 10 months ago

@kaizen89 Sorry for the late. This issue has been fixed now. Please reinstall it by following https://github.com/jinworks/CellChat