Created
September 16, 2014 08:06
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This is a short script to read in Colonyzer2 output after analysis of timecourse images of arrayed microbial cultures growing on solid agar surface. In this case it is assumed that the "time from inoculation" data are stored in the 4th element of an underscore delimited list embedded in the image filenames.
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fnames = list.files(pattern="*.out") | |
datlist = lapply(fnames, read.delim,sep="\t",header=TRUE,stringsAsFactors=FALSE) | |
dat = do.call("rbind", datlist) | |
dat$ID=paste(dat$Barcode,dat$Row,dat$Column,sep="_") | |
dat$time=as.numeric(sapply(strsplit(dat$Filename,'_'), "[", 4)) | |
dat=dat[order(dat$time),] | |
pdf("GrowthCurves.pdf") | |
by(dat,dat$ID,function(x) plot(x$time,x$Intensity,type="b",xlab="Time",ylab="Intensity",ylim=c(0,0.1),main=unique(x$ID))) | |
dev.off() |
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