Download plots, and the combination of ui.R and server.R as app.R

.gitignore

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+plotTreeShiny/.Rproj.user/ED8AE702/sdb/prop/INDEX

plotTreeShiny/.Rhistory

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+setwd("G:/01_Research/Scripts/plotTree/plotTreeShiny")

plotTreeShiny/.Rproj.user/ED8AE702/build_options

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+auto_roxygenize_for_build_and_reload="0"
+auto_roxygenize_for_build_package="1"
+auto_roxygenize_for_check="1"
+makefile_args=""

plotTreeShiny/.Rproj.user/ED8AE702/pcs/files-pane.pper

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+{
+    "path" : "G:/01_Research/Scripts/plotTree/plotTreeShiny",
+    "sortOrder" : [
+        {
+            "ascending" : true,
+            "columnIndex" : 2
+        }
+    ]
+}

plotTreeShiny/.Rproj.user/ED8AE702/pcs/source-pane.pper

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+{
+    "activeTab" : 0
+}

plotTreeShiny/.Rproj.user/ED8AE702/pcs/windowlayoutstate.pper

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+{
+    "left" : {
+        "panelheight" : 998,
+        "splitterpos" : 420,
+        "topwindowstate" : "NORMAL",
+        "windowheight" : 1036
+    },
+    "right" : {
+        "panelheight" : 998,
+        "splitterpos" : 631,
+        "topwindowstate" : "NORMAL",
+        "windowheight" : 1036
+    }
+}

plotTreeShiny/.Rproj.user/ED8AE702/pcs/workbench-pane.pper

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+{
+    "TabSet1" : 0,
+    "TabSet2" : 0
+}

plotTreeShiny/.Rproj.user/ED8AE702/saved_source_markers

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+{"active_set":"","sets":[]}

plotTreeShiny/.Rproj.user/ED8AE702/sdb/prop/BB3849AE

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+{
+}

plotTreeShiny/.Rproj.user/ED8AE702/sdb/prop/FA5A19B6

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+{
+}

plotTreeShiny/checkHash.R

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+checkHash <- function(s) {
+  # This function is designed to fix the problem of wrong colour paramters from the widget jscolorInput.
+  # colorRampPalette() of plotTree() uses col2rgb(), which takes strings like "#FFFFFF" but not "FFFFFF" as the input.
+  # therefore a '#' must be added to the beginnging of every initial input$*_col which does not contain the hash sign.
+  # However, the value picked up from the pop-up palette returns value starting from '#'.
+  # This disconsistancy between return values from the input box and the pop-up palette could be a bug of jscolorInput.
+  # FYI, errors of col2rgb:
+  #   col2rgb("FFFFFF"): invalid color name 'FFFFFF'
+  #   col2rgb("##FFFFFF"): invalid RGB specification
+  if (substring(s, 1, 1) != '#') {  # for values from the input box of jscolorInput
+    return(paste('#', s, sep = ''))
+  } else {
+    return(s)  # for values picked up from the pop-up palette
+  }
+}

plotTreeShiny/plotTree.R

@@ -73,31 +73,16 @@ return(list(m=as.matrix(m),w=w,h=h))
 }
 
 
-plotTree<-function(tree,ladderise=NULL,heatmapData=NULL,barData=NULL,infoFile=NULL,blockFile=NULL,snpFile=NULL,gapChar="?",genome_size=5E6,blwd=5,block_colour="black",snp_colour="red",genome_offset=0,colourNodesBy=NULL,infoCols=NULL,outputPDF=NULL,outputPNG=NULL,w,h,heatmap.colours=rev(gray(seq(0,1,0.1))),tip.labels=F,tipLabelSize=1,offset=0,tip.colour.cex=0.5,legend=T,legend.pos="bottomleft",ancestral.reconstruction=F,cluster=NULL,tipColours=NULL,lwd=1.5,axis=F,axisPos=3,edge.color="black",infoCex=0.8,colLabelCex=0.8,treeWidth=10,infoWidth=10,dataWidth=30,edgeWidth=1,labelHeight=10,mainHeight=100,barDataWidth=10,blockPlotWidth=10,barDataCol=2,heatmapBreaks=NULL,heatmapDecimalPlaces=1,vlines.heatmap=NULL,vlines.heatmap.col=2,heatmap.blocks=NULL,pie.cex=0.5) {
+plotTree<-function(tree,heatmapData=NULL,barData=NULL,infoFile=NULL,blockFile=NULL,snpFile=NULL,gapChar="?",genome_size=5E6,blwd=5,block_colour="black",snp_colour="red",genome_offset=0,colourNodesBy=NULL,infoCols=NULL,outputPDF=NULL,outputPNG=NULL,w,h,heatmap.colours=rev(gray(seq(0,1,0.1))),tip.labels=F,tipLabelSize=1,offset=0,tip.colour.cex=0.5,legend=T,legend.pos="bottomleft",ancestral.reconstruction=F,cluster=NULL,tipColours=NULL,lwd=1.5,axis=F,axisPos=3,edge.color="black",infoCex=0.8,colLabelCex=0.8,treeWidth=10,infoWidth=10,dataWidth=30,edgeWidth=1,labelHeight=10,mainHeight=100,barDataWidth=10,blockPlotWidth=10,barDataCol=2,heatmapBreaks=NULL,heatmapDecimalPlaces=1,vlines.heatmap=NULL,vlines.heatmap.col=2,heatmap.blocks=NULL,pie.cex=0.5) {
 
 require(ape)
 
-# PREPARE TREE, CHOOSE LADDERISATION OR NOT, AND GET TIP ORDER
+# PREPARE TREE AND GET TIP ORDER
 if (is.character(tree)){
 t<-read.tree(tree)
 }
 else t<-tree
-if (is.null(ladderise))
-{
-tl<-t
-}
-else if (ladderise=="descending")
-{
-tl<-ladderize(t, T)
-}
-else if (ladderise=="ascending")
-{
-tl<-ladderize(t, F)
-}
-else if (!is.null(ladderise))
-{
-print("Ladderise option should be exactly 'ascending' or 'descending'.  Any other command will raise this error. Leave option empty to order branches as per input tree.")
-}
+tl<-ladderize(t)
 tips<-tl$edge[,2]
 tip.order<-tips[tips<=length(tl$tip.label)]
 tip.label.order<-tl$tip.label[tip.order] # for ordering data. note that for tiplabel(), the order is the same as in t$tip (= tl$tip)

plotTreeShiny/plotTreeShiny.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Yes
+SaveWorkspace: No
+AlwaysSaveHistory: No
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX