a question about cell grouping file when running spring browser version

[liuweihanty]

Hope your week is going well and thanks for your work on the spring force directed graph online viewer! I have a question regarding the input file "cell groupings". Based on the instruction: I constructed my cell grouping csv files as:

My goal is to visualize the cell identity clusters on the spring plot. So  the first column as the cell identity label followed by cell barcode in the second column. But apparently this is not correct because it returns the error message: Error: Cell grouping "HSC" has a different number of entries (1) than the number of cells (6613) in the expression matrix. I have no luck in googling... would you mind clarifying what exactly should the format be? Thank you very much for your time!

[bug1303]

I'm not a developer, just a user that ran into the same issue...

It actually expects the csv to look like:

celltype, HSC, B, B, B, Neutrophil, Neutrophil, ...

and you could possibly have another line like cluster, 0, 1, 1, 1, 2, 2,

or whatever else you might distinguish your cells by

This is what I did to select some columns from a Seurat object's metadata:

write( paste(c("Sample", as.character(seur.obj$orig.ident)), collapse=","),
       file="groupings.csv")

write( paste(c("SeuratClusters", seur.obj$seurat_clusters), collapse=","),
       file="groupings.csv", 
       append=T)

write( paste(c("CellType", seur.obj$SingleR), collapse=","),
       file="groupings.csv", 
       append=T)

[loversaber]

Really difficult to understand the structure of cell grouping file, does anyone have an idea how to set up it correctly and display cells in different conditions in the plot? Much appreciated!