Update instrument_17_DIA_MS1_counts.R

Fixed bug with the source_file not being initialized. Added missing line of code, so DO-MS is able to start up.

modules/dia-nn/020_Ion_Sampling/instrument_17_DIA_MS1_counts.R

@@ -3,16 +3,17 @@ init <- function() {
   type <- 'plot'
   box_title <- 'Channel-wise MS1 Copy Number for Precursors'
   help_text <- 'Plotting the MS1 copy numbers for all precursors associated with one of the defined channels. The copy numbers are calculated using the signal-to-noise ratio as described in Derks et al. 2022. By default, a resolution of 70,000 is used during preprocessing. It can be changed with the –resolution parameter.'
+  source_file <- 'report'
 
   .validate <- function(data, input) {
-    validate(need(data()[['sn']], paste0('Upload report.txt')))
-    validate(need((nrow(data()[['sn']]) > 1), paste0('No Rows selected')))
+    validate(need(data()[['report']], paste0('Upload report.txt')))
+    validate(need((nrow(data()[['report']]) > 1), paste0('No Rows selected')))
     validate(need(config[['ChemicalLabels']], paste0('Please provide a list of labels under the key: ChemicalLabels in the settings.yaml file')))
 
   }
 
   .plotdata <- function(data, input) {
-    plotdata <- data()[['sn']][,c('Raw.file','Precursor.Id', 'Copy.Number')]
+    plotdata <- data()[['report']][,c('Raw.file','Precursor.Id', 'Copy.Number')]
     plotdata <- translate_diann_channel_format(plotdata, columns = c("Precursor.Id"))
     plotdata <- separate_channel_info(plotdata)