Error in createCellChat object

[lyuguol]

Dear CellChat developers,

I am following your tutorial to do cell-cell communication analysis with my Seurat(V3) data. However, I encountered an error at the first step, and did not figure out why and how to solve it.

Here is how I prepare the data:

data.input <- GetAssayData(scRNA, assay = "RNA", slot = "data")
labels <- Idents(scRNA)
meta <- data.frame(group = labels, row.names = names(labels))
cellchat <- createCellChat(object = data.input, meta = meta, group.by = "labels")

Create a CellChat object from a data matrix
Error in createCellChat(object = data.input, meta = meta, group.by = "labels") :
The 'group.by' is not a column name in the meta, which will be used for cell grouping.

Could you show me how to fix this problem?

Many thanks and best,

Guoliang

[sqjin]

Hi @lyuguol , you should do meta <- data.frame(labels = labels, row.names = names(labels)). You can also directly pass a Seurat object to createCellChat by setting 'group.by = "ident"'. please check the example given in this function.

[lyuguol]

Hi @lyuguol , you should do meta <- data.frame(labels = labels, row.names = names(labels)). You can also directly pass a Seurat object to createCellChat by setting 'group.by = "ident"'. please check the example given in this function.

Many thanks for the quick reply!!!!!
Indeed, solved my problem!!

Best,

Guoliang