Permalink
Switch branches/tags
Nothing to show
Find file Copy path
923367f Apr 28, 2017
1 contributor

Users who have contributed to this file

95 lines (71 sloc) 2.58 KB
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()