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test.R
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test.R
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library(fishplot)
#simple example
timepoints=c(0,30,75,150)
frac.table = matrix(
c(100, 45, 00, 00,
02, 00, 00, 00,
02, 00, 02, 01,
98, 00, 95, 40),
ncol=length(timepoints))
parents = c(0,1,1,3)
fish = createFishObject(frac.table,parents,
timepoints=timepoints,
clone.labels=c("Founding", "Subclone 1","Subclone 2","Subclone 3"))
fish = layoutClones(fish)
sample.times = c(0,150)
pdf("test.out.pdf",width=8,height=4)
fishPlot(fish,shape="spline",title.btm="633734",
vlines=sample.times, vlab=sample.times, cex.title=0.5, bg.type="solid")
drawLegend(fish)
dev <- dev.off()
#recreate figure one from the manuscript
pdf("figure1.pdf",height=6,width=8)
layout(mat=t(matrix(c(1,2,3,3),nrow=2)), widths=c(1,1), heights=c(1,1.5))
##-------------------------------------------
##panel A
timepoints=c(0,30,200,423)
parents = c(0,1,1,3)
frac.table = matrix(
c(100, 38, 24, 00,
002, 00, 01, 00,
002, 00, 01, 01,
100, 00, 98, 30),
ncol=length(timepoints))
fish = createFishObject(frac.table,parents,timepoints=timepoints)
fish = layoutClones(fish)
fishPlot(fish, shape="spline", vlines=c(0,423), vlab=c(0,423), title="Sample 150288", cex.title=0.9, cex.vlab=0.8)
##panel label
text(-100,130,"A",xpd=T,font=2)
##-------------------------------------------
##panel B
parents = c(0,1,2,1)
timepoints=c(0,120)
frac.table = matrix(
c(100, 98, 46, 01,
100, 44, 01, 55),
ncol=length(timepoints))
fish = createFishObject(frac.table,parents,timepoints=timepoints)
fish = layoutClones(fish)
fish = setCol(fish,col=c("#1B9E77","#D95F02","#7570B3","#E7298A"))
fishPlot(fish, shape="polygon", vlab=c("Primary","Post-AI"), vlines=c(0,120), title.btm="BRC32", cex.title=0.7, cex.vlab=0.8,ramp.angle=1, pad.left=0.3)
##panel label
text(-50,130,"B",xpd=T,font=2)
##-------------------------------------------
##panel C
timepoints=c(0,34,69,187,334,505,530)
parents = c(0,1,1,1,3,4,0)
frac.table = matrix(
c(99, 30, 2, 60, 0, 2, 1,
1, 0, 0.1, 00, 0, 0, 1,
3, 0, 2.5, 00, 0, 0, 1,
1, 0, 0.9, 00, 0, 0, 10,
3, 0, 0.9, 00, 0.1, 0, 20,
80, 0, 76, 00, 60, 0, 15,
0.1, 0, 0.005, 00, 0.001, 0, 0),
ncol=7)
fish = createFishObject(frac.table,parents,timepoints=timepoints)
fish = layoutClones(fish, separate.independent.clones=T)
fish = setCol(fish,c("#888888", "#EF0000", "#8FFF40", "#FF6000", "#50FFAF", "#FFCF00", "#0070FF"))
vlines=c(0,34,69,187,334,505,530,650,750)
fishPlot(fish, shape="spline", vlines=vlines, vlab=vlines, title.btm="AML31",cex.vlab=0.9)
##panel label
text(-125,130,"C",xpd=T,font=2)
dev=dev.off()
# testing driver mutation annotations
pdf("figure2.pdf", width=5, height=8)
layout(mat=t(matrix(c(1,2,3), nrow=1,ncol=3)))
##-------------------------------------------
##panel A
timepoints=c(0,30,75,150)
frac.table = matrix(
c(100, 45, 00, 00,
02, 00, 00, 00,
02, 00, 02, 01,
98, 00, 95, 40),
ncol=length(timepoints))
parents = c(0,1,1,3)
fish = createFishObject(frac.table,parents,
timepoints=timepoints,
clone.labels=c("Founding", "Subclone 1","Subclone 2","Subclone 3"),
clone.annots=c("TP53,MET", "NF1", "", "8q+,6p-"))
fish = layoutClones(fish)
sample.times = c(0,150)
fishPlot(fish,shape="spline",title.btm="633734",
vlines=sample.times, vlab=sample.times, cex.title=0.5, bg.type="solid")
##-------------------------------------------
##panel B
timepoints=c(0,30,200,423)
parents = c(0,1,1,3)
frac.table = matrix(
c(100, 38, 24, 00,
002, 00, 01, 00,
002, 00, 01, 01,
100, 00, 98, 30),
ncol=length(timepoints))
fish = createFishObject(frac.table,
parents,
timepoints=timepoints,
clone.annots=c("DNMT3A,FLT3", "NPM1", "MET", "ETV6,WNK1-WAC,\nMYO18B"),
clone.annots.col="green", clone.annots.angle=30)
fish = layoutClones(fish)
fishPlot(fish, shape="spline", vlines=c(0,423), vlab=c(0,423), title="Sample 150288", cex.title=0.9, cex.vlab=0.8)
##panel label
text(-100,130,"A",xpd=T,font=2)
drawLegend(fish)
##-------------------------------------------
##panel C
parents = c(0,1,2,1)
timepoints=c(0,120)
frac.table = matrix(
c(100, 98, 46, 01,
100, 44, 01, 55),
ncol=length(timepoints))
fish = createFishObject(frac.table,parents,timepoints=timepoints)
fish = layoutClones(fish)
fish = setCol(fish,col=c("#1B9E77","#D95F02","#7570B3","#E7298A"))
fish@clone.annots = c("TP53", "", "BRCA", "")
fishPlot(fish, shape="polygon", vlab=c("Primary","Post-AI"),
vlines=c(0,120), title.btm="BRC32",
cex.title=0.7, cex.vlab=0.8,ramp.angle=1, pad.left=0.3)
dev <- dev.off()
##-------------------------------------------
## first example but with modified annotation and legend positioning
timepoints=c(0,30,75,150)
frac.table = matrix(
c(100, 45, 00, 00,
02, 00, 00, 00,
02, 00, 02, 01,
98, 00, 95, 40),
ncol=length(timepoints))
parents = c(0,1,1,3)
clone.labels=c("Founding", "Subclone 1","Subclone 2","Subclone 3")
clone.annots=c("0", "1", "2", "3")
sample.times = c(0,150)
fish = createFishObject(frac.table,parents,
timepoints=timepoints,
clone.labels=clone.labels, clone.annots=clone.annots,
clone.annots.cex=1.5, clone.annots.pos=3, clone.annots.offset=0.5, clone.annots.col="blue")
fish = layoutClones(fish)
fishPlot(fish,shape="spline",title.btm="633734",
vlines=sample.times, vlab=sample.times, cex.title=0.5, bg.type="solid")
drawLegend(fish, xsp=0.3, widthratio=0.1)
##-------------------------------------------
## test if the clones are not listed in order
## see https://github.com/chrisamiller/fishplot/pull/2
pdf("ordertest.pdf", width=8, height=5)
library(fishplot)
timepoints=c(0,30,75,150)
frac.table = matrix(
c(100, 45, 00, 00,
02, 00, 00, 00,
02, 00, 02, 01,
98, 00, 95, 40),
ncol=length(timepoints))
parents = c(0,1,1,3)
##Now just rearrange clones.
frac.table = frac.table[c(4,3,2,1),]
parents = c(2,4,4,0)
fish = createFishObject(frac.table,parents,timepoints=timepoints)
fish = layoutClones(fish)
fishPlot(fish,shape="spline",title.btm="Sample1",
cex.title=0.5, vlines=c(0,150),
vlab=c("day 0","day 150"))
dev <- dev.off()