Fishplot - Updated Clonevol Integration in Additional File 2

run.R

library(sciClone)
library(clonevol)
library(fishplot)

## read in the data - copy number
cn1 = read.table("tumor.cn",sep="\t",stringsAsFactors=F)
cn2 = read.table("relapse.cn",sep="\t",stringsAsFactors=F)
cn1 = cn1[,c(1,2,3,5)]
cn2 = cn2[,c(1,2,3,5)]
## read in vaf data
v1=read.table("tumor.vafs",sep="\t",stringsAsFactors=F,header=T)
v2=read.table("relapse.vafs",sep="\t",stringsAsFactors=F,header=T)

samples = c("Tumor","Relapse")

## run sciclone to detect clusters
sc = sciClone(vafs=list(v1,v2),
              copyNumberCalls=list(cn1,cn2),
              sampleNames=samples,
              useSexChrs=FALSE, doClusteringAlongMargins=FALSE) 
writeClusterTable(sc, "clusters")
sc.plot2d(sc,"clusters.2d.pdf")

## prepare clonevol input
vafs = data.frame(cluster=sc@vafs.merged$cluster,
                  tvaf=sc@vafs.merged$Tumor.vaf,
                  rvaf=sc@vafs.merged$Relapse.vaf,stringsAsFactors=F)
vafs = vafs[!is.na(vafs$cluster) & vafs$cluster > 0,]
names(vafs)[2:3] = samples

## run clonevol
res = infer.clonal.models(variants=vafs, cluster.col.name="cluster", vaf.col.names=samples,
                          subclonal.test="bootstrap", subclonal.test.model="non-parametric",
                          cluster.center="mean", num.boots=1000, founding.cluster=1,
                          min.cluster.vaf=0.01, sum.p=0.01, alpha=0.1, random.seed=63108)

# new clonevol
res = convert.consensus.tree.clone.to.branch(res, branch.scale='sqrt')

# new clonevol
plot.clonal.models(res, box.plot=TRUE, fancy.boxplot=TRUE, cell.plot=TRUE,
                   out.format="pdf", overwrite.output=TRUE, scale.monoclonal.cell.frac=TRUE,
                   cell.frac.ci=TRUE, tree.node.shape="circle", tree.node.size=40,
                   tree.node.text.size=0.65, width=8, height=5, out.dir=".")

## create a list of fish objects - one for each model (in this case, there's only one)
f = generateFishplotInputs(results=res)
fishes = createFishPlotObjects(f)

## plot each of these with fishplot
pdf('fish.pdf', width=8, height=4)
for (i in 1:length(fishes)){
    fish = layoutClones(fishes[[i]])
    fish = setCol(fish,f$clonevol.clone.colors)
    fishPlot(fish,shape="spline", title.btm="PatientID", cex.title=0.7,
             vlines=seq(1, length(samples)), vlab=samples, pad.left=0.5)
}
dev <- dev.off()

when I run this script with the tumor and relapse data, has a error:

plot.clonal.models(res$models, matched=res$matched, variants=vafs, box.plot=TRUE,

•                out.format="pdf", overwrite.output=TRUE, scale.monoclonal.cell.frac=TRUE,
  

•                cell.frac.ci=TRUE, tree.node.shape="circle", tree.node.size=40,
  

•                tree.node.text.size=0.65, width=8, height=5, out.dir=".")
  

Error in data.frame(x = c(xstarts, xstops), index = seq(1, 2 * k)) :
arguments imply differing number of rows: 0, 2
In addition: Warning message:
In min(xstarts) : no non-missing arguments to min; returning Inf