HI：
Thank you very much for developing SingleR package.
I have some issue when I creating my Single.R object， I was wondering if could provide me some advices.
when I use the SingleR.PlotTsne function,i get some error like this:
Error in $<-.data.frame(*tmp*, "x", value = c(SC098_675998 = 10.2433937537515, :
replacement has 7214 rows, data has 7067
Here is my code:
singler = CreateSinglerObject(SC098_data, annot = NULL, "SC098", min.genes = 500,technology = "BD", species = "Mouse", citation = "", ref.list = list(immgen), normalize.gene.length = F, variable.genes = "de",fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = T, reduce.file.size = T, numCores = SingleR.numCores)
singler$seurat = SC098
singler$meta.data$orig.ident = SC098@meta.data$orig.ident
singler$meta.data$xy = SC098@reductions$tsne@cell.embeddings
singler$meta.data$clusters = SC098@active.ident
out = SingleR.PlotTsne(singler$singler[[1]]$SingleR.single,singler$meta.data$xy,do.label = F,do.letters = T,labels = singler$singler[[1]]$SingleR.single.main$labels,dot.size = 1.3,alpha=0.5,label.size = 6)
Look forward to your soonest reply
Thank U
Ns
HI： Thank you very much for developing SingleR package. I have some issue when I creating my Single.R object， I was wondering if could provide me some advices. when I use the SingleR.PlotTsne function,i get some error like this: Error in
$<-.data.frame(*tmp*, "x", value = c(SC098_675998 = 10.2433937537515, : replacement has 7214 rows, data has 7067 Here is my code: singler = CreateSinglerObject(SC098_data, annot = NULL, "SC098", min.genes = 500,technology = "BD", species = "Mouse", citation = "", ref.list = list(immgen), normalize.gene.length = F, variable.genes = "de",fine.tune = T, do.signatures = T, clusters = NULL, do.main.types = T, reduce.file.size = T, numCores = SingleR.numCores) singler$seurat = SC098 singler$meta.data$orig.ident = SC098@meta.data$orig.ident singler$meta.data$xy = SC098@reductions$tsne@cell.embeddings singler$meta.data$clusters = SC098@active.identout = SingleR.PlotTsne(singler$singler[[1]]$SingleR.single,singler$meta.data$xy,do.label = F,do.letters = T,labels = singler$singler[[1]]$SingleR.single.main$labels,dot.size = 1.3,alpha=0.5,label.size = 6) Look forward to your soonest reply Thank U Ns