fixed problem with missing parameters, closes #12

ParkerICI · May 11, 2018 · c428bd7 · c428bd7
1 parent b3e949e
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Showing 37 changed files with 12 additions and 40 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,10 @@
 Package: premessa
 Type: Package
 Title: R package for pre-processing of flow and mass cytometry data
-Version: 0.1.5
+Version: 0.1.6
 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, jsonlite
 License: GPL v3
 LazyData: TRUE
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
diff --git a/README.md b/README.md
@@ -80,7 +80,7 @@ To stop the software simply hit the "ESC" key in your R session.
 
 ## Usage
 
-Once you have selected the working directory, the software will extract the panel information from all the FCS files contained in the directory. This information is then displayed in a table, where each row corresponds to a different parameter name ($PnN keyword), indicated by the row names (leftmost column), and each column corresponds to a different file, indicated in the column header. Each cell represents the description string ($PnS keyword) of a specific parameter in a given file. If a parameter is missing from a file, an *NA* is displayed in the corresponding cell, which will be colored orange.
+Once you have selected the working directory, the software will extract the panel information from all the FCS files contained in the directory. This information is then displayed in a table, where each row corresponds to a different parameter name ($PnN keyword), indicated by the row names (leftmost column), and each column corresponds to a different file, indicated in the column header. Each cell represents the description string ($PnS keyword) of a specific parameter in a given file. If a parameter is missing from a file, the word *absent* is displayed in the corresponding cell, which will be colored orange (note that this means that *absent* cannot be a valid parameter name)
 
 The table begins with three special columns:
 - *Remove*: if the box is checked the corresponding parameter is removed from all the files, and the row is grayed out

diff --git a/inst/paneleditor_shinyGUI/server.R b/inst/paneleditor_shinyGUI/server.R
@@ -54,7 +54,7 @@ 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("absent", NA, df[, i])
                 df$Remove <- as.logical(df$Remove)
 
 
@@ -78,7 +78,13 @@ shinyServer(function(input, output, session) {
     })
 
     output$paneleditorui_panel_table <- rhandsontable::renderRHandsontable({
-        df <- data.frame(Remove = FALSE, panel.table, check.names = F, stringsAsFactors = F)
+        temp <- panel.table
+
+        for(i in 1:ncol(temp))
+            temp[, i][is.na(temp[, i])] <- "absent"
+
+        df <- data.frame(Remove = FALSE, temp, check.names = F, stringsAsFactors = F)
+
 
         hot <- rhandsontable::rhandsontable(df, rowHeaderWidth = 100)
         hot <- rhandsontable::hot_cols(hot, fixedColumnsLeft = 3, renderer = "
@@ -92,7 +98,7 @@ shinyServer(function(input, output, session) {
                         if(instance.params.data[row][0])
                             td.style.background = 'lightgrey'
                         else {
-                            if(value == 'NA')
+                            if(value == 'absent')
                                 td.style.background = 'orange'
                             else if(value != instance.params.data[row][2] && col > 2)
                                 td.style.background = 'lightpink'

diff --git a/man/as_flowFrame.Rd b/man/as_flowFrame.Rd
diff --git a/man/calculate_baseline.Rd b/man/calculate_baseline.Rd
diff --git a/man/calculate_bcs_separation.Rd b/man/calculate_bcs_separation.Rd
diff --git a/man/copy_keywords.Rd b/man/copy_keywords.Rd
diff --git a/man/correct_data_channels.Rd b/man/correct_data_channels.Rd
diff --git a/man/debarcode_data.Rd b/man/debarcode_data.Rd
diff --git a/man/debarcode_data_matrix.Rd b/man/debarcode_data_matrix.Rd
diff --git a/man/debarcode_fcs.Rd b/man/debarcode_fcs.Rd
diff --git a/man/debarcoder_GUI.Rd b/man/debarcoder_GUI.Rd
diff --git a/man/get_assignments_at_threshold.Rd b/man/get_assignments_at_threshold.Rd
diff --git a/man/get_barcode_channels_names.Rd b/man/get_barcode_channels_names.Rd
diff --git a/man/get_mahalanobis_distance.Rd b/man/get_mahalanobis_distance.Rd
diff --git a/man/get_mahalanobis_distance_from_beads.Rd b/man/get_mahalanobis_distance_from_beads.Rd
diff --git a/man/get_sample_idx.Rd b/man/get_sample_idx.Rd
diff --git a/man/get_well_abundances.Rd b/man/get_well_abundances.Rd
diff --git a/man/identify_beads.Rd b/man/identify_beads.Rd
diff --git a/man/normalize_by_pop.Rd b/man/normalize_by_pop.Rd
diff --git a/man/normalize_folder.Rd b/man/normalize_folder.Rd
diff --git a/man/normalizer_GUI.Rd b/man/normalizer_GUI.Rd
diff --git a/man/plot_all_barcode_biaxials.Rd b/man/plot_all_barcode_biaxials.Rd
diff --git a/man/plot_barcode_channels_intensities.Rd b/man/plot_barcode_channels_intensities.Rd
diff --git a/man/plot_barcode_separation.Rd b/man/plot_barcode_separation.Rd
diff --git a/man/plot_barcode_yields.Rd b/man/plot_barcode_yields.Rd
diff --git a/man/plot_distance_from_beads.Rd b/man/plot_distance_from_beads.Rd
diff --git a/man/plot_separation_histogram.Rd b/man/plot_separation_histogram.Rd
diff --git a/man/premessa.Rd b/man/premessa.Rd
diff --git a/man/read_barcode_key.Rd b/man/read_barcode_key.Rd
diff --git a/man/read_parameters.Rd b/man/read_parameters.Rd
diff --git a/man/remove_beads_from_fcs.Rd b/man/remove_beads_from_fcs.Rd
diff --git a/man/remove_beads_from_file.Rd b/man/remove_beads_from_file.Rd
diff --git a/man/rename_fcs_parameters_desc.Rd b/man/rename_fcs_parameters_desc.Rd
diff --git a/man/rename_fcs_parameters_name.Rd b/man/rename_fcs_parameters_name.Rd
diff --git a/man/rename_parameters_in_files.Rd b/man/rename_parameters_in_files.Rd
diff --git a/man/write_flowFrame.Rd b/man/write_flowFrame.Rd