Hi, in the ImportCountData() function, if there's '-' in the sample name, it's being changed into '.' which make it incompatible with the barcode names made using ImportHistologicalAnnotations() and the same sample name.
I'd suggest swiping the order of lines 16 and 17, to prevent it.
Such as:
ImportCountData <- function(SectionName, InputCountFile) {
input <- Read10X_h5(InputCountFile, use.names = FALSE)
input <- as.matrix(input)
input <- as.data.frame(t(input))
input <- rownames_tocolumn(input, "Barcode")
input$Barcode <- gsub("\-", "\.", input$Barcode)
input$Barcode <- paste0(SectionName, "", input$Barcode)
return(input)
}
Hi, in the ImportCountData() function, if there's '-' in the sample name, it's being changed into '.' which make it incompatible with the barcode names made using ImportHistologicalAnnotations() and the same sample name.
I'd suggest swiping the order of lines 16 and 17, to prevent it. Such as: ImportCountData <- function(SectionName, InputCountFile) { input <- Read10X_h5(InputCountFile, use.names = FALSE) input <- as.matrix(input) input <- as.data.frame(t(input)) input <- rownames_tocolumn(input, "Barcode") input$Barcode <- gsub("\-", "\.", input$Barcode) input$Barcode <- paste0(SectionName, "", input$Barcode) return(input) }
it doesn't intefere with the rest of the code