networkScatter.R not found

[ssmadha]

I'm trying to run coltron and I'm running into the error: Fatal error: cannot open file 'networkScatter.R': No such file or directory I've looked for this file, but can't seem to find it. I was wondering if maybe I was just missing something?

[GryderArt]

This is the R code you need for that:

#

140521

Federation

#

library(ggplot2)

args = commandArgs(TRUE) degFile = args[1] sizeTable = args[2] output = args[3]

degreeData = read.delim(degFile) sortedDegreeData = degreeData[order(degreeData$Total_Connections, decreasing=T),] sortedDegreeData = sortedDegreeData[1:60,]

TFnames = as.character(sortedDegreeData$Tf) TFandSuperTable = read.delim(sizeTable)

Make the scatter with points based on enhancer size

m = matrix(nrow=length(sortedDegreeData$Tf),ncol=3) rownames(m) = sortedDegreeData$Tf colnames(m) = c('In','Out','Length') m[,1] = sortedDegreeData$In_Degree m[,2] = sortedDegreeData$Out_Degree m[,3] = rep(0,length(TFnames))

for(i in seq(length(row.names(TFandSuperTable)))) { gene = as.character(TFandSuperTable[i,2]) if(is.element(gene, TFnames)) { m[gene,3] =+ (TFandSuperTable[i,7]) } }

pdf(output) qplot(m[,1],m[,2], size=m[,3],label=rownames(m)) + geom_text(parse=T, size=4, hjust=-0.2, vjust=-0.2, position=position_jitter(h=1,w=1)) + labs(x = 'Inward Binding', y='Outward Binding') + theme_bw() + theme(axis.line = element_line(colour = "black"), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.border = element_blank(), panel.background = element_blank())

dev.off()

[ssmadha]

Thank you very much, it works.