minor update

tischi · Mar 11, 2016 · 35c6e6f · 35c6e6f
1 parent 9cee540
commit 35c6e6f
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Showing 4 changed files with 25 additions and 57 deletions.
diff --git a/gui.R b/gui.R
@@ -690,8 +690,8 @@ guiHandler_JitterPlot <- function(h,...){
   gp <- ggroup(horizontal = T, container=w)
   glabel("Experiment selection:  ", container=gp)
   guiExpSubset <- gcombobox(c("None selected", experiments), 
-                  container = gp, 
                   selected = htmGetListSetting(htm,"visualisation","jitterPlotExpSubset",gui=T), 
+                  container = gp, 
                   handler = function(h,...){
                     htmSetListSetting(htm,"visualisation","jitterPlotExpSubset",svalue(h$obj),gui=T)
                   })
@@ -706,14 +706,7 @@ guiHandler_JitterPlot <- function(h,...){
 
   gp <- ggroup(horizontal = T, container=w)
   glabel("Sorting:  ", container=gp)
-  guiSorting <- gcombobox(c("none","alphabetic","median value"), 
-                          container = gp, 
-                          selected = htmGetListSetting(htm,"visualisation","jitterPlot_sorting",gui=T), 
-                          handler = function(h,...){
-                            htmSetListSetting(htm, "visualisation","jitterPlot_sorting",svalue(h$obj),gui=T)
-                          }
-  )
-
+  guiSorting <- gcombobox(c("None selected","alphabetic","median value"), container=gp)
 
   gp <- ggroup(horizontal = T, container=w)
   glabel("Compute t-test against:  ", container=gp)
@@ -728,10 +721,10 @@ guiHandler_JitterPlot <- function(h,...){
                   cx = svalue(cx),
                   cy = svalue(cy),
                   .ylab = svalue(cy),
-                  datatype = htmGetListSetting(htm,"visualisation","jitterPlot_datatype",gui=T),
+                  datatype = svalue(guiSelectedData),
                   experimentSubset = svalue(guiExpSubset),
                   treatmentSubset = htmGetVectorSettings("visualisation$treatmentSelectionForPlotting"),
-                  sorting = htmGetListSetting(htm,"visualisation","jitterPlot_sorting",gui=T),
+                  sorting = svalue(guiSorting),
                   colorizeTreatments = htmGetListSetting(htm,"visualisation","jitterPlot_colorizeTreatments_TF",gui=T), 
                   showMedian = htmGetListSetting(htm,"visualisation","jitterPlot_showMedianAndMAD_TF",gui=T),
                   showMean = htmGetListSetting(htm,"visualisation","jitterPlot_showMeanAndSD_TF",gui=T),
@@ -745,9 +738,9 @@ guiHandler_JitterPlot <- function(h,...){
       htm <- get("htm", envir = globalenv())
       htmJitterplot(htm, svalue(cx), svalue(cy), .xlim=sort(loc$x),.ylim=sort(loc$y),.ylab=svalue(cy),
                     experimentSubset = svalue(guiExpSubset), 
-                    datatype = htmGetListSetting(htm,"visualisation","jitterPlot_datatype",gui=T),
+                    datatype = svalue(guiSelectedData),
                     colorizeTreatments = htmGetListSetting(htm,"visualisation","jitterPlot_colorizeTreatments_TF",gui=T), 
-                    sorting = htmGetListSetting(htm,"visualisation","jitterPlot_sorting",gui=T),
+                    sorting = svalue(guiSorting),
                     newdev = F,
                     treatmentSubset = htmGetVectorSettings("visualisation$treatmentSelectionForPlotting"),
                     showMedian = htmGetListSetting(htm,"visualisation","jitterPlot_showMedianAndMAD_TF",gui=T),
@@ -766,7 +759,7 @@ guiHandler_JitterPlot <- function(h,...){
                     svalue(cx),svalue(cy),.xlim=sort(loc$x),.ylim=sort(loc$y),
                     experimentSubset = svalue(guiExpSubset), 
                     colorizeTreatments = htmGetListSetting(htm,"visualisation","jitterPlot_colorizeTreatments_TF",gui=T), 
-                    sorting = htmGetListSetting(htm,"visualisation","jitterPlot_sorting",gui=T),
+                    sorting = svalue(guiSorting),
                     datatype = svalue(guiSelectedData),
                     newdev = F, action="click",
                     treatmentSubset = htmGetVectorSettings("visualisation$treatmentSelectionForPlotting")
@@ -836,16 +829,7 @@ guiHandler_JitterPlot_Options <- function(h,...) {
             container = w, 
             handler = function(h,...){
               htmSetListSetting(htm, "visualisation","jitterPlot_log2_TF",svalue(h$obj),gui=T)
-            })
-
-  glabel("x axis font size factor:", container=w)
-  gcombobox(c("0.3","0.4","0.5","0.6","0.7","0.8","0.9","1.0"), 
-                          container = w, 
-                          selected = htmGetListSetting(htm,"visualisation","jitterPlot_x_axis_font_size",gui=T), 
-                          handler = function(h,...){
-                            htmSetListSetting(htm, "visualisation","jitterPlot_x_axis_font_size",svalue(h$obj),gui=T)
-                          }
-  )
+            })    
 
   visible(w) <- T
 }
@@ -1129,15 +1113,10 @@ guiHandler_SetColumns <- function(h, ...) {
 
   gbutton(" Apply ", container = gg, handler = function(h,...) {
     htm <- get("htm", envir = globalenv()) 
-    # auto-make batch_treat and treat_batch
     cTreat = htmGetListSetting(htm,"columns","treatment",gui=T)
     cBatch = htmGetListSetting(htm,"columns","experiment",gui=T)
     htm@data$Metadata_batch_treatment = paste(htm@data[[cBatch]],htm@data[[cTreat]],sep="__")
     print(paste("Generated new colum Metadata_batch_treatment, combining",cBatch,"and",cTreat))
-    htm@data$Metadata_treatment_batch = paste(htm@data[[cTreat]],htm@data[[cBatch]],sep="__")
-    print(paste("Generated new colum Metadata_treatment_batch, combining",cTreat,"and",cBatch))
-
-
     assign("htm", htm, envir = globalenv())   
     dispose(w)
   })

diff --git a/india.pdf b/india.pdf
diff --git a/plots.R b/plots.R
@@ -61,11 +61,9 @@ htmShowImagesFromRow <- function(htm,data,irs,appendCommand=""){
   filenamePrefix = htm@settings@visualisation$image_filename_prefix
   foldernamePrefix = htm@settings@visualisation$image_foldername_prefix
   # convert to forward slashes immideately, otherwise gsub has problems later
-  rootFolderTable = gsub("\\\\" ,"/",htmGetListSetting(htm,"visualisation","image_root_foldername_in_table",gui=T))
-  rootFolderReal = gsub("\\\\" ,"/",htmGetListSetting(htm,"visualisation","image_root_foldername_on_this_computer",gui=T))  
-  print(paste("  Pattern in table:",rootFolderTable))
-  print(paste("  Pattern for real:",rootFolderReal))
-
+  rootFolderTable = gsub("\\\\" ,"/",htm@settings@visualisation$image_root_foldername_in_table)
+  rootFolderReal = gsub("\\\\" ,"/",htm@settings@visualisation$image_root_foldername_on_this_computer)  
+
   if( .Platform$OS.type == "unix" ) {
     #imageViewerCMD = "/Applications/Fiji.app/Contents/MacOS/fiji-macosx --no-splash"
     imageViewerCMD = '/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx -debug '
@@ -90,13 +88,10 @@ htmShowImagesFromRow <- function(htm,data,irs,appendCommand=""){
           imagename = strsplit(colname,filenamePrefix)[[1]][2]
           filename = data[[colname]][ir]
           cFolder = paste(foldernamePrefix,imagename,sep="")
-          foldername = data[[cFolder]][ir]
-          print(paste("  Folder in table:",foldername))
-          foldername = gsub("\\\\" ,"/", foldername)
-          #print(paste("  Folder after replacement of slashes:",foldername))
+          #print(cFolder)
+          foldername = gsub("\\\\" ,"/",data[[cFolder]][ir])
           foldername = gsub(rootFolderTable, rootFolderReal, foldername)
-          print(paste("  Folder after subsitution of local mapping:",foldername))
-
+
           if ( .Platform$OS.type == "unix" ) {
             #foldername = gsub("\\\\" ,"/", foldername)
             #pathname = paste('"',foldername,"/",filename,'"',sep="")
@@ -703,7 +698,7 @@ htmHeatmap_MarkSelectedTreatment <- function(htm, selectedExp, selectedTreatment
 
 htmJitterplot <- function(htm=htm, cx, cy, .xlab="", .ylab="", treatmentSubset = "None selected", 
                           .xlim=NA, .ylim=NA, datatype="images", colorizeTreatments=F,  
-                          sorting="none", experimentSubset="None selected", newdev = T, 
+                          sorting="None selected", experimentSubset="None selected", newdev = T, 
                           action="plot", printMeanSD = T,  showMean = T, showMedian = T, save2file = F,
                           scaleFromZero = F, reference="None selected") {
 
@@ -777,7 +772,7 @@ htmJitterplot <- function(htm=htm, cx, cy, .xlab="", .ylab="", treatmentSubset =
   }
 
   print(paste("  sorting:",sorting))
-  if(sorting=="none") {
+  if(sorting=="None selected") {
     ids = 1:nrow(data)
   }
   if(sorting=="alphabetic") {
@@ -946,12 +941,7 @@ htmJitterplot <- function(htm=htm, cx, cy, .xlab="", .ylab="", treatmentSubset =
     } else {  # zooming  
       plot(jp.x, jp.y, xaxt = "n", xlab=.xlab, ylab=.ylab, xlim=.xlim, ylim=.ylim, pch=pchQC, cex=dotsize, col=.colors,  cex.lab =1)
     }
-    if(htmGetListSetting(htm,"visualisation","jitterPlot_x_axis_font_size",gui=T) != "None selected") {
-      x_axis_font_size = as.numeric(htmGetListSetting(htm,"visualisation","jitterPlot_x_axis_font_size",gui=T))
-    } else {
-      x_axis_font_size = 1
-    }
-    axis(1, at=1:length(lx), labels=lx, las=2,  cex.axis = x_axis_font_size)
+    axis(1, at=1:length(lx), labels=lx, las=2,  cex.axis = 1)
 
     plotTitle = ""
     if(experimentSubset[1] != "None selected") {

diff --git a/run.R b/run.R
@@ -1,24 +1,23 @@
 
+## specify libraries
+libs = list("gWidgets","gWidgetstcltk","markdown","plyr")
 
 ## install libraries
-if(F) {
-  install.packages("gWidgets", repos='http://cran.us.r-project.org')
-  install.packages("gWidgetstcltk", repos='http://cran.us.r-project.org')
-  install.packages("markdown", repos='http://cran.us.r-project.org')
-  install.packages("plyr", repos='http://cran.us.r-project.org')
-}
+# sapply(libs, biocLite) 
+# install.packages("gWidgets")
+# install.packages("gWidgetstcltk")
+# install.packages("markdown")
+# install.packages("plyr")
+
 
 ## load libraries
 print("Loading libraries...")
-libs = list("gWidgets","gWidgetstcltk","markdown","plyr")
 sapply(libs, function(x) do.call("library", list(x))) 
 
 options(warn = 2)
 
 # path = "C:\\Users\\Christian Tischer\\Dropbox\\R\\HTM\\HTM_Explorer\\HTM_Explorer";setwd(path);source("run.R");
 # path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R"); 
-# path = "\\\\almf\\almf\\software\\scripts\\R\\HTM_Explorer";setwd(path);source("run.R");
-# path = "Y:\\R\\HTM_Explorer";setwd(path);source("run.R");
 
 ## source code
 #setwd(path);source("install.R");