[R] barchart producing incorrect number of barcharts when columns renamed

[Colm G. Connolly]

On 25 Apr 2007, at 19:50, Deepayan Sarkar wrote:

> 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.
>

Indeed you are correct. My apologies.

This more minimal code should demonstrate the problem. I've removed  
all references to external files and verified that I have the same  
problem without them.

When I change the column names I get a 4x4 array of barcharts,  
whereas when I do not change the column names I correctly get the 5x5  
array.

The question is what causes this discrepancy?

library('lattice')
rm(list=ls())

textFontSize=6;

clipping="(NOT Clipped)";

roi.errs=data.frame(
   cbind(
         ##Group
         c("ctrl", "ctrl", "short", "short", "long", "long"),
         ##Subject
         c("66101_2", "66112_2", "66119", "66121", "66026_3",  
"66030_2")),
   cbind(
         ##Sub-brick
         c(0, 0, 0, 0, 0, 0),
         ##Mean_1
         c(0.546532, 6.057756, 0.241484, 8.861095, 6.712401, 6.714763),
         ##Mean_2
         c(0.541001, 1.821168, -0.071227, 7.387406, 4.164371, 6.196456),
         ##Mean_3
         c(-0.211658, 1.053770, 4.772759, 9.780944, 7.530651, 3.357583),
         ##Mean_4
         c(0.592144, -2.386457, 4.998830, 12.428849, 14.037164,  
4.049794),
         ##Mean_5
         c(1.449212, 2.445002, -2.718933, 8.900946, 7.919560, 8.350304),
         ##Mean_6
         c(1.919896, 2.466083, -3.906275, 0.822132, 5.910088, 4.678836),
         ##Mean_7
         c(0.665386, -3.790489, 1.191782, 3.613919, 3.808240, 5.036492),
         ##Mean_8
         c(0.865090, 1.741351, 2.012702, 10.093662, 0.829254, 3.880265),
         ##Mean_9
         c(0.342638, -1.200232, 9.458908, 7.756559, 6.308535, 1.497788),
         ##Mean_10
         c(1.522509, 1.780352, 4.471669, -1.122842, 4.923762, 4.025056),
         ##Mean_11
         c(0.615833, 1.363775, 0.215138, 5.988049, 7.545206, 2.117970),
         ##Mean_12
         c(-0.932574, -1.140839, -5.778118, 5.749871, 8.312596,  
4.937120),
         ##Mean_13
         c(-1.403353, 9.795787, 1.129139, 2.383282, 4.998841, 3.721432),
         ##Mean_14
         c(0.534640, 4.651436, -0.163107, 3.714310, 6.594728, 3.636995),
         ##Mean_15
         c(0.951416, 2.384751, -2.804867, 4.662075, 4.375787, 5.767994),
         ##Mean_16
         c(0.333624, -4.837685, -2.951958, -3.335181, 2.915522,  
2.617556),
         ##Mean_17
         c(2.184298, 7.578843, -2.862990, 6.923186, -2.569342,  
0.913788),
         ##Mean_18
         c(0.382605, 6.441820, 0.579722, -2.424237, 6.884646, 3.127198),
         ##Mean_19
         c(-0.737142, 3.306980, 2.417347, -7.521070, 6.570706,  
1.556814),
         ##Mean_20
         c(0.545103, 8.721134, -1.766060, 21.433794, 5.829050,  
4.031095)));

colnames(roi.errs)=c("Group","Subject","Sub- 
brick","Mean_1","Mean_2","Mean_3","Mean_4","Mean_5","Mean_6","Mean_7",
"Mean_8","Mean_9","Mean_10","Mean_11","Mean_12","Mean_13","Mean_14","Mea 
n_15","Mean_16","Mean_17","Mean_18",
"Mean_19","Mean_20");

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.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)

#####################################
### WITH column name change
#####################################

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) = list("R Cing Gy", "R Smar Gy", "L Inf Fron Gy",
           "R Thalamus", "R Mid Fron Gy", "L Mid Temp Gy", "L Inf Par  
Lbl",
           "R Mid Fron Gy", "L Cing Gy", "R Thalamus", "R Mid Fron  
Gy", "R Lent Nuc",
           "R Inf Fron Gy", "R Mid Temp Gy", "R Sup Par Lbl", "R Cere  
Ton",
           "L Prec", "R Cere Ton", "L Pyramis", "R Prec Gy");

cat("errs.Means dimensions after col name change ", dim(errs.Means),  
"\n");

get(getOption("device"))()
fontsize=trellis.par.get("fontsize");
fontsize$text=textFontSize;
trellis.par.set("fontsize", fontsize);

print(barchart(errs.Means, groups=rownames(errs.Means), xlab='Mean  
Intensity',
                main=paste("Mean Cluster Intensity for Errors",  
clipping),
                ylab='Group', col=rainbow(length(rownames 
(errs.Means))), border=rainbow(length(rownames(errs.Means)))))

#####################################
### WITHOUT column name change
#####################################

errs.Means=rbind(roi.errs.ctrl.means, roi.errs.short.means,  
roi.errs.long.means)
rownames(errs.Means)=c('control', 'short', 'long')

get(getOption("device"))()
fontsize=trellis.par.get("fontsize");
fontsize$text=textFontSize;
trellis.par.set("fontsize", fontsize);

print(barchart(errs.Means, groups=rownames(errs.Means), xlab='Mean  
Intensity',
                main=paste("Mean Cluster Intensity for Errors",  
clipping),
                ylab='Group', col=rainbow(length(rownames 
(errs.Means))), border=rainbow(length(rownames(errs.Means)))))

Thanks,

Regards,
--
Dr Colm G. Connolly
School of Psychology and Institute of Neuroscience
The Lloyd Building
University of Dublin
Trinity College, Dublin 2, Éire
Tel: +353-1-896-8475
Fax: +353-1-671-3183