36 lines
1.9 KiB
R
36 lines
1.9 KiB
R
# Requires gplots, gregmisc package. split.file() output files.
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# See Burton-Kelly (2008) for complete documentation.
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confplotvbar<-function(path, pattern, vardis="Variation", barnames=c(1:20),xlabel="Genus", reps=1000, ext="-confplotvbar.txt", probs=c(0.025,0.975))
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{
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require(gplots);
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files<-list.files(path=path,pattern=pattern,full.names=TRUE);
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for(i in files)
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#Loop through files and assign variable names [This is not necessary]
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{
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x <- read.table(i,header=TRUE);
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assign(i, x);
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}
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for(j in 1:length(files))
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{
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SOV <- get(files[j]);
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bootSOV <- numeric(reps);
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#creates place for bootstrap values
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for (k in 1:reps) {bootSOV[k] <- sum(diag(var(sample(SOV, replace=TRUE))))};
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conf<-quantile(bootSOV,probs=probs);
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toplot<-paste(barnames[j],mean(bootSOV), conf[2],conf[1],files[j]);
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write.table(toplot,file=paste(substring(files[1],1, nchar(files[1])-4), ext, sep=""),quote=FALSE,append=TRUE, row.names=FALSE,col.names=FALSE)
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}
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tableback<-read.table(file=paste(substring(files[1],1, nchar(files[1])-4), ext, sep=""));
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x<-unlist(tableback[1]);
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y<-unlist(tableback[2]);
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cui<-unlist(tableback[3]);
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cli<-unlist(tableback[4]);
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barplot2(height=y,names.arg=x,xlab=xlabel, ylab=vardis,ci.l=cli,ci.u=cui,plot.ci=TRUE);
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pdf(paste(substring(files[1],1,nchar(files[1])-4), ext, c(".pdf"), sep=""));
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barplot2(height=y,names.arg=x,xlab=xlabel,ylab=vardis,ci.l=cli,ci.u=cui,plot.ci=TRUE);
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dev.off();
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file.rename(paste(substring(files[1],1,nchar(files[1])-4), ext, sep=""),paste(path,"/confplotvbar-",pattern,".txt",sep=""));
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file.rename(paste(substring(files[1],1,nchar(files[1])-4), ext, c(".pdf"), sep=""),paste(path,"/confplotvbar-", pattern,".pdf",sep=""));
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# If using OS X, can announce when done
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# system("say All done!");
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} |