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Commit 3086d52

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schultzm
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Added ladderise options to both the plotTree.R standalone script, and to the plotTree.R shiny version. Changes added at lines 76 and lines 84 to 100.
1 parent 8b5546f commit 3086d52

2 files changed

Lines changed: 36 additions & 6 deletions

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‎plotTree.R‎

Lines changed: 18 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -73,16 +73,31 @@ return(list(m=as.matrix(m),w=w,h=h))
7373
}
7474

7575

76-
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) {
76+
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) {
7777

7878
require(ape)
7979

80-
# PREPARE TREE AND GET TIP ORDER
80+
# PREPARE TREE, CHOOSE LADDERISATION OR NOT, AND GET TIP ORDER
8181
if (is.character(tree)){
8282
t<-read.tree(tree)
8383
}
8484
else t<-tree
85-
tl<-ladderize(t)
85+
if (is.null(ladderise))
86+
{
87+
tl<-t
88+
}
89+
else if (ladderise=="descending")
90+
{
91+
tl<-ladderize(t, T)
92+
}
93+
else if (ladderise=="ascending")
94+
{
95+
tl<-ladderize(t, F)
96+
}
97+
else if (!is.null(ladderise))
98+
{
99+
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.")
100+
}
86101
tips<-tl$edge[,2]
87102
tip.order<-tips[tips<=length(tl$tip.label)]
88103
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/plotTree.R‎

Lines changed: 18 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -73,16 +73,31 @@ return(list(m=as.matrix(m),w=w,h=h))
7373
}
7474

7575

76-
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) {
76+
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) {
7777

7878
require(ape)
7979

80-
# PREPARE TREE AND GET TIP ORDER
80+
# PREPARE TREE, CHOOSE LADDERISATION OR NOT, AND GET TIP ORDER
8181
if (is.character(tree)){
8282
t<-read.tree(tree)
8383
}
8484
else t<-tree
85-
tl<-ladderize(t)
85+
if (is.null(ladderise))
86+
{
87+
tl<-t
88+
}
89+
else if (ladderise=="descending")
90+
{
91+
tl<-ladderize(t, T)
92+
}
93+
else if (ladderise=="ascending")
94+
{
95+
tl<-ladderize(t, F)
96+
}
97+
else if (!is.null(ladderise))
98+
{
99+
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.")
100+
}
86101
tips<-tl$edge[,2]
87102
tip.order<-tips[tips<=length(tl$tip.label)]
88103
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)

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