Merge branch 'master' of github.com:uzh/ezRun

uzh · Oct 23, 2020 · 6ac8f91 · 6ac8f91
2 parents b7435af + 159895d
commit 6ac8f91
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Showing 2 changed files with 9 additions and 6 deletions.
diff --git a/R/ngsio.r b/R/ngsio.r
@@ -16,7 +16,10 @@ loadCountDataset <- function(input, param){
   dataFeatureLevel <- unique(input$getColumn("featureLevel"))
   stopifnot(length(dataFeatureLevel) == 1)
 
-  x1 <- read_tsv(files[1], guess_max=1e6)
+  x1 <- read_tsv(files[1], guess_max=1e6,  col_types = cols())
+  ## col type messages are suppressed by col_types = cols()
+  ## Alternatively: The message is triggered by readr:::show_cols_spec. 
+  ##To suppress the message, put this at the top of your script: options(readr.num_columns = 0)
 
   if (ezIsSpecified(param$expressionName)){
     columnName <- param$expressionName
@@ -33,7 +36,7 @@ loadCountDataset <- function(input, param){
 
   x <- mapply(function(x, y){
     message("loading file: ", x)
-    tempTibble <- read_tsv(x, progress=FALSE, guess_max=1e6)
+    tempTibble <- read_tsv(x, progress=FALSE, guess_max=1e6, col_types = cols())
     tempTibble %>%
       dplyr::select(identifier, columnName) %>%
       dplyr::rename("id":= 1, !! y := columnName)

diff --git a/inst/templates/CountQC.Rmd b/inst/templates/CountQC.Rmd
@@ -158,7 +158,7 @@ if(!is.null(rowData(rawData)$gene_name)){
 write_xlsx(counts, path=countFile)
 # normalized signal
 signalFile <- paste0(ezValidFilename(param$name), "-normalized-signal.xlsx")
-write_xlsx(combined, file=signalFile, head="Feature ID", digits=4)
+write_xlsx(combined, path=signalFile)
 
 selectSignals = grepl("Signal", colnames(combined))
 combined$"Mean signal" = rowMeans(combined[, selectSignals], na.rm=TRUE)
@@ -177,7 +177,7 @@ combined = combined[order(combined$"Maximum signal", decreasing = TRUE), ,
 useInInteractiveTable = c("seqid", "gene_name", "Maximum signal", 
                           "Mean signal", "description", "featWidth", "gc")
 useInInteractiveTable = intersect(useInInteractiveTable, colnames(combined))
-tableLink = sub(".txt", "-viewHighExpressionGenes.html", signalFile)
+tableLink = sub(".xlsx", "-viewHighExpressionGenes.html", signalFile)
 ## select top genes
 combinedTopGenes = combined[which(rownames(combined) %in% topGenes),]
 ## restrict number of table rows if necessary
@@ -190,7 +190,7 @@ ezInteractiveTable(interactiveTable, tableLink=tableLink, digits=3,
                    title=paste("Showing the top", nRows, 
                                "genes with the highest expression"))
 
-rpkmFile <- paste0(ezValidFilename(param$name), "-rpkm.txt")
+rpkmFile <- paste0(ezValidFilename(param$name), "-rpkm.xlsx")
 rpkm <- as_tibble(getRpkm(rawData), rownames="Feature ID")
 if(!is.null(rowData(rawData)$gene_name)){
   rpkm <- left_join(rpkm,
@@ -213,7 +213,7 @@ write_xlsx(tpm, path=tpmFile)
 ```
 
 ```{r add data files link, echo=FALSE, results='asis', message=FALSE}
-for(each in dataFiles){
+for(each in c(countFile, signalFile, rpkmFile, tpmFile, tableLink)){
   cat("\n")
   cat(paste0("[", each, "](", each, ")"))
   cat("\n")