Fix Time issues

saeyslab · Aug 18, 2023 · f2f847d · f2f847d
1 parent 0a04a08
commit f2f847d
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Showing 4 changed files with 24 additions and 11 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: PeacoQC
 Title: Peak-based selection of high quality cytometry data
-Version: 1.11.1
+Version: 1.11.2
 Authors@R: 
     person(given = "Annelies",
            family = "Emmaneel",

diff --git a/NEWS b/NEWS
@@ -1,3 +1,9 @@
+PeacoQC (version 1.11.2)
+------------------------
+
+Fix time bugs
+================================================================================
+
 PeacoQC (version 1.11.1)
 ------------------------
 

diff --git a/R/PeacoQC.R b/R/PeacoQC.R
@@ -644,9 +644,14 @@ PlotPeacoQC <- function(ff,
 
     # Check for time channel
     if (!is.null(time_channel_parameter)){
+        if (all(!grepl(time_channel_parameter,
+                  colnames(flowCore::exprs(ff)),
+                  ignore.case=TRUE))){
+            time_channel <- NULL
+        } else{
         time_channel <- grep(time_channel_parameter,
                              colnames(flowCore::exprs(ff)),
-                             ignore.case=TRUE)
+                             ignore.case=TRUE)}
     } else(time_channel <-  NULL)
 
     if (is.numeric(channels)){
@@ -687,9 +692,11 @@ PlotPeacoQC <- function(ff,
     if (!is.null(time_channel)){
         if (is(display_peaks, "list") && display_peaks$Analysis != FALSE){
             p_time <- BuildTimePlot(ff, blocks$overview_blocks_time,
-                                    scores_time, time_unit)
+                                    scores_time, time_unit,
+                                    time_id = time_channel)
         } else{ p_time <- BuildTimePlot(ff, scores_time=scores_time,
-                                        time_unit=time_unit) }
+                                        time_unit=time_unit,
+                                        time_id = time_channel) }
 
         plot_list[["Time"]] <- p_time
 

diff --git a/R/PlotPeacoQC_helper_functions.R b/R/PlotPeacoQC_helper_functions.R
@@ -37,9 +37,9 @@ MakeOverviewBlocks <- function(ff, peaks, time_channel){
     overview_blocks_time <- NULL
     if (length(time_channel) > 0){
 
-        x_min <- flowCore::exprs(ff)[, "Time"][c(1,
+        x_min <- flowCore::exprs(ff)[, time_channel][c(1,
             cumsum(run_length$lengths)[-length(run_length$lengths)])]
-        x_max <- flowCore::exprs(ff)[, "Time"][cumsum(run_length$lengths)]
+        x_max <- flowCore::exprs(ff)[, time_channel][cumsum(run_length$lengths)]
 
         overview_blocks_time <- data.frame(x_min=x_min,
                                             x_max=x_max,
@@ -75,21 +75,21 @@ MakeManualBlocks <- function(manual_cells){
 }
 
 
-BuildTimePlot <- function(ff, blocks=NULL, scores_time, time_unit=100){
+BuildTimePlot <- function(ff, blocks=NULL, scores_time, time_unit=100, time_id){
     if (nrow(ff) >=50000) {
         subset_timeplot <- sort(sample(seq_len(nrow(ff)), 50000))
     } else {
         subset_timeplot <- seq_len(nrow(ff))
     }
 
 
-    h <- graphics::hist(flowCore::exprs(ff)[subset_timeplot, "Time"],
-                        breaks=seq(min(flowCore::exprs(ff)[, "Time"]),
-                                        max(flowCore::exprs(ff)[, "Time"]) +
+    h <- graphics::hist(flowCore::exprs(ff)[subset_timeplot, time_id],
+                        breaks=seq(min(flowCore::exprs(ff)[, time_id]),
+                                        max(flowCore::exprs(ff)[, time_id]) +
                                         time_unit, by=time_unit),
                         plot=FALSE)
 
-    idcs <- findInterval(flowCore::exprs(ff)[subset_timeplot, "Time"], h$breaks)
+    idcs <- findInterval(flowCore::exprs(ff)[subset_timeplot, time_id], h$breaks)
 
     p_time <- ggplot() + theme_bw()