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mattbk
2015-08-16 14:58:49 -05:00
parent e69edb519a
commit 52198ac043
4 changed files with 120 additions and 0 deletions
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confplotvbar.R Normal file
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# Requires gplots, gregmisc package. split.file() output files.
# See Burton-Kelly (2008) for complete documentation.
confplotvbar<-function(path, pattern, vardis="Variation", barnames=c(1:20),xlabel="Genus", reps=1000, ext="-confplotvbar.txt", probs=c(0.025,0.975))
{
require(gplots);
files<-list.files(path=path,pattern=pattern,full.names=TRUE);
for(i in files)
#Loop through files and assign variable names [This is not necessary]
{
x <- read.table(i,header=TRUE);
assign(i, x);
}
for(j in 1:length(files))
{
SOV <- get(files[j]);
bootSOV <- numeric(reps);
#creates place for bootstrap values
for (k in 1:reps) {bootSOV[k] <- sum(diag(var(sample(SOV, replace=TRUE))))};
conf<-quantile(bootSOV,probs=probs);
toplot<-paste(barnames[j],mean(bootSOV), conf[2],conf[1],files[j]);
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)
}
tableback<-read.table(file=paste(substring(files[1],1, nchar(files[1])-4), ext, sep=""));
x<-unlist(tableback[1]);
y<-unlist(tableback[2]);
cui<-unlist(tableback[3]);
cli<-unlist(tableback[4]);
barplot2(height=y,names.arg=x,xlab=xlabel, ylab=vardis,ci.l=cli,ci.u=cui,plot.ci=TRUE);
pdf(paste(substring(files[1],1,nchar(files[1])-4), ext, c(".pdf"), sep=""));
barplot2(height=y,names.arg=x,xlab=xlabel,ylab=vardis,ci.l=cli,ci.u=cui,plot.ci=TRUE);
dev.off();
file.rename(paste(substring(files[1],1,nchar(files[1])-4), ext, sep=""),paste(path,"/confplotvbar-",pattern,".txt",sep=""));
file.rename(paste(substring(files[1],1,nchar(files[1])-4), ext, c(".pdf"), sep=""),paste(path,"/confplotvbar-", pattern,".pdf",sep=""));
# If using OS X, can announce when done
# system("say All done!");
}