v.0.3.11

Author: quantixed

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TrackMateR
 Type: Package
 Title: Working with TrackMate outputs in R
-Version: 0.3.10
+Version: 0.3.11
 Authors@R:
     person(given = "Stephen J",
            family = "Royle",
@@ -14,7 +14,7 @@ Description: TrackMate, a plugin for ImageJ/Fiji, is a popular single-particle t
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends: R (>= 2.10)
 Config/rcmdcheck/ignore-inconsequential-notes: true
 VignetteBuilder:

NEWS.md

@@ -1,5 +1,9 @@
 # TrackMateR
 
+# TrackMateR 0.3.11
+
+- Better handling of more than one channel in TrackMate XML files
+
 # TrackMateR 0.3.10
 
 - Fixed an issue where sparse TrackMate XML files caused `compareDatasets()` to fail

R/readTrackMateXML.r

@@ -44,6 +44,10 @@ readTrackMateXML<- function(XMLpath){
   if(unitVec[1] == "pixel") {
     cat("Spatial units are in pixels - consider transforming to real units\n")
   }
+  # which channel is being tracked?
+  targetVec <-  xpathSApply(e, "//DetectorSettings", xmlGetAttr, "TARGET_CHANNEL")
+  calibrationDF[7,1] <- as.numeric(targetVec)
+  calibrationDF[7,2] <- "channel"
 
   # multicore processing
   numCores <- parallelly::availableCores()
@@ -78,7 +82,7 @@ readTrackMateXML<- function(XMLpath){
   # more R-like headers
   headerNames <- tolower(attrName)
   # remove _CH1 or whatever from headers
-  headerNames <- gsub("\\wCH\\d$","",headerNames,ignore.case = T)
+  # headerNames <- gsub("\\wCH\\d$","",headerNames,ignore.case = T)
   # change x y z t
   headerNames <- gsub("^position\\w","",headerNames,ignore.case = T)
   names(dtf) <- headerNames

R/tm_plots.R

@@ -168,27 +168,38 @@ plot_tm_displacementHist <- function(input, summary = FALSE, xstr = NULL, ystr =
 #' @param auto boolean to switch between returning a ggplot and a list of ggplot and variable
 #' @return ggplot or list of ggplot and variable
 #' @export
-plot_tm_intensityHist <- function(input, summary = FALSE, xstr = NULL, ystr = NULL, auto = FALSE) {
+plot_tm_intensityHist <- function(input, summary = FALSE, xstr = "Intensity (AU)", ystr = "Frequency", auto = FALSE) {
   dataid <- trace <- mean_intensity <- intensity <- NULL
 
   if(inherits(input, "list")) {
     df <- input[[1]]
     calibration <- input[[2]]
     units <- calibration$unit[1:2]
-    xstr <- "Intensity (AU)"
-    ystr <- "Frequency"
+    # get the channel from calibration dataframe by using the value in column 1 where in column 2 it has the value "channel"
+    ch <- calibration$value[calibration$unit == "channel"]
   } else {
     df <- input
   }
 
+  # the column containing mean_intensity may not be present in the data frame
+  # if it is present we will use that column, if not we will use paste0("mean_intensity_ch",ch)
+  # and if that doesn't exist we will use "mean_intensity_ch1"
+  if("mean_intensity" %in% colnames(df)) {
+    mean_intensity_col <- "mean_intensity"
+  } else if(paste0("mean_intensity_ch", ch) %in% colnames(df)) {
+    mean_intensity_col <- paste0("mean_intensity_ch", ch)
+  } else {
+    mean_intensity_col <- "mean_intensity_ch1"
+  }
+
   if(summary) {
     intDF <- df %>%
       group_by(dataid, trace) %>%
-      summarise(intensity = max(mean_intensity))
+      summarise(intensity = max(!!sym(mean_intensity_col), na.rm = TRUE))
   } else {
     intDF <- df %>%
       group_by(trace) %>%
-      summarise(intensity = max(mean_intensity))
+      summarise(intensity = max(!!sym(mean_intensity_col), na.rm = TRUE))
   }
 
   median_int <- median(intDF$intensity, na.rm = TRUE)