convertSingleR2Browser error

[danshu]

Hi,

After generating singler, there is an error running "convertSingleR2Browser". Here is the error message: Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length

convertSingleR2Browser function (singler, use.singler.cluster.annot = T) { ref.names = unlist(lapply(singler$singler, FUN = function(x) x$about$RefData)) cell.names = rownames(singler$singler[[1]]$SingleR.single$labels) labels = as.data.frame(sapply(singler$singler, FUN = function(x) x$SingleR.single$labels)) if (!is.null(singler$singler[[1]]$SingleR.single.main)) { labels.main = as.data.frame(sapply(singler$singler, FUN = function(x) x$SingleR.single.main$labels)) labels = cbind(labels, labels.main) colnames(labels) = c(ref.names, paste0(ref.names, ".main")) } else { colnames(labels) = c(ref.names) } rownames(labels) = cell.names 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$labels1)) labels1 = cbind(labels1, labels1.main) colnames(labels1) = c(ref.names, paste0(ref.names, ".main")) } else { colnames(labels1) = c(ref.names) } rownames(labels1) = cell.names } labels.clusters = data.frame() labels.clusters1 = data.frame() if (use.singler.cluster.annot == T) { if (length(levels(singler$meta.data$clusters)) > 1) { if (!is.null(singler$singler[[1]]$SingleR.clusters)) { labels.clusters = as.data.frame(sapply(singler$singler, FUN = function(x) x$SingleR.clusters$labels)) if (!is.null(singler$singler[[1]]$SingleR.clusters.main)) { labels.clusters.main = as.data.frame(sapply(singler$singler, FUN = function(x) x$SingleR.clusters.main$labels)) labels.clusters = cbind(labels.clusters, labels.clusters.main) colnames(labels.clusters) = c(ref.names, paste0(ref.names, ".main")) } else { colnames(labels.clusters) = c(ref.names) } rownames(labels.clusters) = levels(singler$meta.data$clusters) } if (!is.null(singler$singler[[1]]$SingleR.cluster$labels1)) { if (!is.null(singler$singler[[1]]$SingleR.clusters)) { labels.clusters1 = as.data.frame(sapply(singler$singler, FUN = function(x) x$SingleR.clusters$labels1)) if (!is.null(singler$singler[[1]]$SingleR.clusters.main)) { labels.clusters.main = as.data.frame(sapply(singler$singler, FUN = function(x) x$SingleR.clusters.main$labels1)) labels.clusters1 = cbind(labels.clusters1, labels.clusters.main) colnames(labels.clusters1) = c(ref.names, paste0(ref.names, ".main")) } else { colnames(labels.clusters1) = c(ref.names) } rownames(labels.clusters1) = levels(singler$meta.data$clusters) } } } } scores = lapply(singler$singler, FUN = function(x) x$SingleR.single$scores) if (!is.null(singler$singler[[1]]$SingleR.single.main)) { scores.main = lapply(singler$singler, FUN = function(x) x$SingleR.single.main$scores) scores = c(scores, scores.main) names(scores) = c(ref.names, paste0(ref.names, ".main")) } else { names(scores) = c(ref.names) } clusters = data.frame(clusters = singler$meta.data$clusters) rownames(clusters) = cell.names ident = data.frame(orig.ident = singler$meta.data$orig.ident) rownames(ident) = cell.names singler.small = new("SingleR", project.name = singler$meta.data$project.name, xy = singler$meta.data$xy, labels = labels, labels.NFT = labels1, labels.clusters = labels.clusters, labels.clusters.NFT = labels.clusters1, scores = scores, clusters = clusters, ident = ident, other = data.frame(singler$signatures), expr = singler$seurat@data, meta.data = c(Citation = singler$singler[[1]]$about$Citation, Organism = singler$singler[[1]]$about$Organism, Technology = singler$singler[[1]]$about$Technology)) singler.small } <bytecode: 0x561ba82a9c18>

Best, Danshu

[dviraran]

Its kind of impossible to guess... you pasted the function code, and the error doesn't say much. Only suggestion I can make is that you post your SingleR object (a small version of it - run it with a small subset of cells).

[danshu]

Its kind of impossible to guess... you pasted the function code, and the error doesn't say much. Only suggestion I can make is that you post your SingleR object (a small version of it - run it with a small subset of cells).

test.nGene200.zip Thanks for your reply! Here is a test case using 100 cells.

[dviraran]

Yeah, its failing because you don't have a field 'clusters' in meta.data. You need it for some functionalities in the browser.

Just do something like this:

singler$meta.data$clusters = factor(clusters)

with whatever cluster ids you have.

[danshu]

singler$meta.data$clusters <- as.character(1:100) singler.new = convertSingleR2Browser(singler) Error in initialize(value, ...) : trying to get slot "data" from an object of a basic class ("NULL") with no slots singler$meta.data$clusters <- factor(1:100) singler.new = convertSingleR2Browser(singler) Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length

Still having errors after assigning clusters

[dviraran]

Apparently, this function assumed the use of the SInglerSeurat pipeline. I removed this assumption in a new version I just deployed. It works for me on your file.

You can avoid using clusters altogether by setting the variable 'use.singler.cluster.annot' to FALSE.

[danshu]

Thanks! It works now!