closes #5

ParkerICI · Sep 25, 2017 · 23b5651 · 23b5651
1 parent a213ff6
commit 23b5651
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: premessa
 Type: Package
 Title: R package for pre-processing of flow and mass cytometry data
-Version: 0.1.1
+Version: 0.1.2
 Author: "Pier Federico Gherardini <pfgherardini@parkerici.org> [aut, cre]"
 Description: This package includes panel editing/renaming for FCS files, bead-based normalization and debarcoding.
 Imports: shiny (>= 0.14), flowCore, reshape, ggplot2, hexbin, gridExtra, rhandsontable

diff --git a/R/paneleditor_helpers.R b/R/paneleditor_helpers.R
@@ -118,6 +118,7 @@ rename_parameters_in_files <- function(working.dir, out.dir, tab) {
     file.cols <- grep("Remove|Parameter", names(tab), invert = T)
     for(i in file.cols) {
         f.name <- file.path(working.dir, names(tab)[i])
+        print(sprintf("Processing %s ...", f.name))
         fcs <- read_fcs(f.name)
         to.remove <- row.names(tab)[tab$Remove]
         if(length(to.remove) > 0)
@@ -127,7 +128,6 @@ rename_parameters_in_files <- function(working.dir, out.dir, tab) {
         names.map <- tab$Parameter
         names(names.map) <- row.names(tab)
         fcs <- rename_fcs_parameters_name(fcs, names.map)
-
         names.map <- tab[, i]
         names(names.map) <- tab$Parameter
         names.map <- names.map[!is.na(tab[, i])]

diff --git a/inst/paneleditor_shinyGUI/server.R b/inst/paneleditor_shinyGUI/server.R
@@ -55,7 +55,7 @@ shinyServer(function(input, output, session) {
             isolate({
                 df <- rhandsontable::hot_to_r(input$paneleditorui_panel_table)
                 for(i in 1:ncol(df))
-                    df[, i] <- gsub("NA", NA, df[, i])
+                    df[, i] <- gsub("^NA$", NA, df[, i])
                 df$Remove <- as.logical(df$Remove)