Converting conos object to Seurat fails about seurat-wrappers

[akramdi]

I actually forgot to check/fix duplicated cell names across samples before Conos integration...
For anyone with the same issue, here's how I fixed it (I used CheckDuplicateCellNames from Seurat):

## Check if we have duplicated cell names. If yes, fix it
if ( any(duplicated(unlist(lapply(objectList,colnames)))) ){
  objectList <- Seurat:::CheckDuplicateCellNames(objectList)
}

After running Conos integration, the conversion to Seurat works perfectly.

[akramdi]

Hi,

I have the same issue:

sobj <- as.Seurat(con)
Merging 10 samples
Adding pairwise alignments to 'conos.pairs' in miscellaneous data
Adding graph as 'SCT_mnn'
Error in intI(i, n = d[1], dn[[1]], give.dn = FALSE) : 
  invalid character indexing
In addition: Warning message:
In CheckDuplicateCellNames(object.list = objects) :
  Some cell names are duplicated across objects provided. Renaming to enforce unique cell names.

Were you finally able to convert from Conos to Seurat ?
Thanks,

[akramdi]

Well, I was able to spot the code that causes the error in as.Seurat function:

seurat-wrappers/R/conos.R

Lines 75 to 80 in 156e392

	# Add graph
	if (!is.null(x = x$graph)) {
	graph <- paste(DefaultAssay(object = object), method, sep = '_')
	message("Adding graph as '", graph, "'")
	object[[graph]] <- as.Graph(x = get.adjacency(graph = x$graph)[colnames(x = object), colnames(x = object)])
	}

Precisely in line 79:

object[[graph]] <- as.Graph(x = get.adjacency(graph = x$graph)[colnames(x = object), colnames(x = object)])
Error in intI(i, n = d[1], dn[[1]], give.dn = FALSE) :
invalid character indexing

Cell names retrieved bycolnames(object) do not match cell names present in the matrix returned by get.adjacency(graph = x$graph).

> colnames(object) %>% head()
[1] "AAACCCAAGGCGTCCT_1" "AAACCCACAACAGCCC_1" "AAACGAAAGCTTGTTG_1"
[4] "AAACGAACAGACACCC_1" "AAACGAAGTAACTTCG_1" "AAACGCTAGCGATGCA_1"

> head(get.adjacency(graph = con$graph))
6 x 20199 sparse Matrix of class "dgCMatrix"
   [[ suppressing 34 column names ‘ACCCTTGCAGCAGATG’, ‘AAACCCATCTAGACAC’, ‘CTGGTCTGTACACGCC’ ... ]]

I'm not sure at which level this can be efficiency fixed. Can one of the developers give some advice ?

Thanks,

[vtosevski]

Hi Amira,

I had not followed it further back then. I will keep this in mind next time I come around to it, it would be a very simple fix. Thanks for checking it more carefully.

Vinko