Open akhst7 opened 5 years ago
Look at the code of that function and run it line-by-line, find where its failing and fix it.
I got the same issue here, while I used only one Seurat object. Here's the code:
singler = CreateSinglerObject(counts = seuratObj$SCT@data, ...)
singler$meta.data$orig.ident = seuratObj@active.ident
singler$meta.data$xy = seuratObj@reductions$umap@cell.embeddings # umap, instead of tSNE
singler$meta.data$clusters = seuratObj@active.ident
singler.new = convertSingleR2Browser(singler)
Error in
.rowNamesDF<-
(x, value = value) : invalid 'row.names' length
Please advise. Thanks!
@dviraran and @sunkh1026
I have not carefully looked at this yet, but the issue appears to be the very first part of convertSingleR2Browser. Here is a traceback;
6: stop("invalid 'row.names' length")
5: .rowNamesDF<-
(x, value = value)
4: row.names<-.data.frame
(*tmp*
, value = value)
3: row.names<-
(*tmp*
, value = value)
2: rownames<-
(*tmp*
, value = cell.names)
1: convertSingleR2Browser(PA.combined.singler)`
This part of code gives an error;
`labels1 = data.frame() if (!is.null(singler$singler[[1]]$SingleR.single$labels1)) { labels1 = as.data.frame(sapply(singler$singler, FUN = function(x) x$SingleR.single$labels1)) if (!is.null(singler$singler[[1]]$SingleR.single.main)) { labels1.main = as.data.frame(sapply(singler$singler, FUN = function(x) x$SingleR.single.main$labels1)) labels1 = cbind(labels1, labels1.main) colnames(labels1) = c(ref.names, paste0(ref.names, ".main")) } else { colnames(labels1) = c(ref.names) }
rownames(labels1) = cell.names }`
The only thing I can find is that label1 and label has different dimension;
dim(labels1) [1] 13436 4
dim(labels) [1] 15677 6
This is pretty much as far as I can go at this point. I really need a pointer to fix this.
Thanks.
Hi All, I am also struggling with the same issue. Did you guys manage to solve this issue? Kindly share your troubleshooting experience.
Thanks in advance
@bharati16mehani,
I don't think this issue is solved but you can use the new SingleR version and plot similar t-SNE or UMAP plots by using ggplot2 or ggpubr or write your own Shiny scripts, then you don't need this web resource.
So I successfully created a singler object from the combined/integrated Seurat object but I can't convert it to upload and visualize it in the SinglerR website. I get this effort message;
Error in
.rowNamesDF<-(x, value = value) : invalid 'row.names' length
I know why I get this, coming from virtually two Seruat objects together . Is there any way to get over this so I can visualize data ?
Thanks.