Colm G. Connolly
2007-Apr-25 14:35 UTC
[R] barchart producing incorrect number of barcharts when columns renamed
Hi everybody,
I'm having problems with the barchart command in the lattice package.
I'm creating barcharts from matrices with with anything from 20 to 71
columns. When I leave the column names alone, that is they are set in
the read.table command (and inherited by subsequent commands) the
correct number barcharts is created by the "print(barchart(...))"
command. However, when I reset the column names by means of a scan
command, the number of barcharts drawn by the same command is
incorrect: it is always too few. The scan commands produce lists the
same length as the number of columns for which I want barcharts.
In total I've got four pages with barcharts. The numbers in the table
below indicate the number of barcharts per page. The numbers without
() are the number of barcharts that I expect (and get when I don't
reset the column titles). The numbers in () are the numbers of
barcharts I get when I reset the column titles.
Not Clipped Clipped
Errs 20 (18) 71 (46)
Stops 32 (24) 46 (36)
The following is the code used to create the barcharts with sample
text output below it.
library('lattice')
rm(list=ls())
textFontSize=6;
pdf('../data/cocaineBarcharts.pdf', paper='a4')
fontsize=trellis.par.get("fontsize");
fontsize$text=textFontSize;
trellis.par.set("fontsize", fontsize);
resultsDirs=c("../data/Group.results.noclipping", "../data/
Group.results.clipped");
#resultsDirs=c("../data/Group.results.clipped");
for (resultsDir in resultsDirs) {
cat(resultsDir, "\n")
if (any(grep("clipped", resultsDir)))
{
clipping="(Clipped)";
}
else
{
clipping="(NOT Clipped)";
}
roi.errs=read.table(paste(resultsDir,
"allGroupsROI.acrossGroupWithinEvent.errs", sep="/"),
header=T, sep="");
roi.errs.names=names(roi.errs);
# ctrl
roi.errs.ctrl<-roi.errs[roi.errs[,"Group"]=="ctrl",
4:length
(roi.errs)]
roi.errs.ctrl.subjects=roi.errs[roi.errs[,"Group"]=="ctrl",
2]
# short
roi.errs.short<-roi.errs[roi.errs[,"Group"]=="short",
4:length
(roi.errs)]
roi.errs.short.subjects=roi.errs[roi.errs[,"Group"]=="short",
2]
# long
roi.errs.long<-roi.errs[roi.errs[,"Group"]=="long",
4:length
(roi.errs)]
roi.errs.long.subjects=roi.errs[roi.errs[,"Group"]=="long",
2]
roi.stops=read.table(paste(resultsDir,
"allGroupsROI.acrossGroupWithinEvent.stops", sep="/"),
header=T,
sep="");
roi.stops.names=names(roi.stops);
# ctrl
roi.stops.ctrl<-roi.stops[roi.stops[,"Group"]=="ctrl",
4:length
(roi.stops)]
roi.stops.ctrl.subjects=roi.stops[roi.stops[,"Group"]=="ctrl",
2]
# short
roi.stops.short<-roi.stops[roi.stops[,"Group"]=="short",
4:length
(roi.stops)]
roi.stops.short.subjects=roi.stops[roi.stops[,"Group"]=="short",
2]
# long
roi.stops.long<-roi.stops[roi.stops[,"Group"]=="long",
4:length
(roi.stops)]
roi.stops.long.subjects=roi.stops[roi.stops[,"Group"]=="long",
2]
#matrixToPlot=as.matrix(roi.errs.ctrl[1:5,])
#yylim=c(floor(min(matrixToPlot)), ceiling(max(matrixToPlot)))
#barplot(matrixToPlot, col=c(2:6), beside=T, ylim=yylim,
names.arg=colnames(roi.errs.ctrl),
# border=c(2:6), legend.text=roi.errs$Subject[1:5])
roi.errs.ctrl.matrix=as.matrix(roi.errs.ctrl)
roi.errs.short.matrix=as.matrix(roi.errs.short)
roi.errs.long.matrix=as.matrix(roi.errs.long)
roi.stops.ctrl.matrix=as.matrix(roi.stops.ctrl)
roi.stops.short.matrix=as.matrix(roi.stops.short)
roi.stops.long.matrix=as.matrix(roi.stops.long)
#####################################################################
### errors
#####################################################################
# pdf(paste(resultsDir, 'errorsByGroup.pdf', sep="/"),
paper='a4')
# fontsize=trellis.par.get("fontsize");
# fontsize$text=textFontSize;
# trellis.par.set("fontsize", fontsize);
roi.errs.ctrl.means=colMeans(roi.errs.ctrl.matrix)
roi.errs.short.means=colMeans(roi.errs.short.matrix)
roi.errs.long.means=colMeans(roi.errs.long.matrix)
yylim=c(floor(min(roi.errs[, 4:length(roi.errs)])), ceiling(max
(roi.errs[, 4:length(roi.errs)])))
errs.Means=rbind(roi.errs.ctrl.means, roi.errs.short.means,
roi.errs.long.means)
rownames(errs.Means)=c('control', 'short', 'long')
cat("errs.Means dimensions before col name change ", dim
(errs.Means), "\n");
colnames(errs.Means) = scan(paste(resultsDir,
"clusterLocations.errs.csv", sep="/"), sep=",",
what="character")
cat("errs.Means dimensions after col name change ", dim
(errs.Means), "\n");
print(barchart(errs.Means, groups=rownames(errs.Means), xlab='Mean
Intensity',
main=paste("Mean Cluster Intensity for Errors",
clipping),
ylab='Group', col=rainbow(3), border=rainbow(3)))
# dev.off()
#####################################################################
### Stops
#####################################################################
# pdf(paste(resultsDir, 'stopsByGroup.pdf', sep="/"),
paper='a4')
# fontsize=trellis.par.get("fontsize");
# fontsize$text=textFontSize;
# trellis.par.set("fontsize", fontsize);
roi.stops.ctrl.means=colMeans(roi.stops.ctrl.matrix)
roi.stops.short.means=colMeans(roi.stops.short.matrix)
roi.stops.long.means=colMeans(roi.stops.long.matrix)
yylim=c(floor(min(roi.stops[, 4:length(roi.stops)])), ceiling(max
(roi.stops[, 4:length(roi.stops)])))
stops.Means=rbind(roi.stops.ctrl.means, roi.stops.short.means,
roi.stops.long.means)
rownames(stops.Means)=c('control', 'short', 'long')
cat( "stops.Means dimensions before col name change ", dim
(stops.Means), "\n");
colnames(stops.Means) = scan(paste(resultsDir,
"clusterLocations.stops.csv", sep="/"), sep=",",
what="character")
cat( "stops.Means dimensions after col name change ", dim
(stops.Means), "\n");
print(barchart(stops.Means, groups=rownames(stops.Means),
xlab='Mean Intensity',
main=paste("Mean Cluster Intensity for Stops",
clipping),
ylab='Group', col=rainbow(3), border=rainbow(3)))
# dev.off()
}
dev.off()
Sample output:
../data/Group.results.noclipping
errs.Means dimensions before col name change 3 20
Read 20 items
errs.Means dimensions after col name change 3 20
stops.Means dimensions before col name change 3 32
Read 32 items
stops.Means dimensions after col name change 3 32
../data/Group.results.clipped
errs.Means dimensions before col name change 3 71
Read 71 items
errs.Means dimensions after col name change 3 71
stops.Means dimensions before col name change 3 46
Read 46 items
stops.Means dimensions after col name change 3 46
The text file storing the names for the columns is created by a perl
script and is in comma separated value format.
Can some please tell me what I've done wrong?
Thank in advance,
Regards,
--
Dr Colm G. Connolly
School of Psychology and Institute of Neuroscience
The Lloyd Building
University of Dublin
Trinity College, Dublin 2, ?ire
Tel: +353-1-896-8475
Fax: +353-1-671-3183
Deepayan Sarkar
2007-Apr-25 18:50 UTC
[R] barchart producing incorrect number of barcharts when columns renamed
On 4/25/07, Colm G. Connolly <Colm.Connolly at tcd.ie> wrote:> Hi everybody, > > I'm having problems with the barchart command in the lattice package. > > [... ... ...] > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.You seem to have missed this footer that appears in every r-help message. Your code is not reproducible, and not minimal by a long, long, shot. -Deepayan