plot - no main title and missing abscissa value

Iain Gallagher wrote:

Hi. Sorry (esp to Uwe for the repeated messages!)

Here is the data and my code in full. Thanks for the
help.

Data.

Day    Ym1Imp    Ym1sham    Semimp    Semsham
0    5.78    5.78    1.22    1.36
1    44.36    42.1    16.26    18.83
3    38.39    14.66    18.02    2.86
5    57.76    1.03    15.28    0.29
7    72.93    2.71    18.6    1.06
10    48.57    4.61    11.26    5.21
14    74.08    1.53    9.66    0.11
21    73.86    0.14    7.2    0.02


Code

ym<- read.table("ym1expression.csv", header=T,
sep="\t", quote="\"") #read in ym data
attach(ym)# make data visible to R
par(mar=c(5,5,4,5),las=1, xpd=NA)
x<- c(0,1,3,5,7,10,14,21)
plot(Day, Ym1Imp, ylim=c(0,100), type="b", bty="l",
main="Ym1 Expression", cex=1.3, xaxt="n", yaxt="n")
#plot implant data
axis(side=1, at=c(0,1,3,5,7,10,14,21),
labels=c(0,1,3,5,7,10,14,21)) # label x axis
mtext("Day", side =1, at=10, line=3, cex=1.2) # title
x axis
mtext("AU", side=2, at=50, line=3, cex=1.2)# y axis
title
axis(side=2, at=c(0, 25, 50, 75, 100),
labels=expression("0", "25", "50", "75", "100")) #
label y axis
arrows(x, Ym1Imp-Semimp, x, Ym1Imp+Semimp, code=3,
angle=90, length=0.1)# place error bars
points(Day, Ym1sham, type="b", pch=16, cex=1.3)# plot
sham data
arrows(x, Ym1sham-Semsham, x, Ym1sham+Semsham, code=3,
angle=90, length=0.1)# plot sham error bars
legend(20, 60, legend="Implant", pch=1, lty=1,
bty="n")# implant legend
legend(20, 50, legend="Sham", pch=16, lty=1, bty="n")#
sham legend

Iain

Three points:

1. The main title appears for me under the Windows device. I really 
wonder why you do not see it, this seems to be quite a strange device 
dependence I would not expect in this case.
Since you told us you have "R 2.1", we do not know exactly what you 
have got - there is no such version. There are versions R-2.0.1, 
R-2.1.0 and R-2.1.1, though. Anyway, you told us you found a workaround.


2. In order to re-plot the axis labels, you should specify  xlab=NA, 
ylab=NA in your call to plot() as in:
plot(Day, Ym1Imp, ylim=c(0,100), type="b", bty="l", xlab=NA, ylab=NA,
    main="Ym1 Expression", cex=1.3, xaxt="n", yaxt="n")

3. As I have already guessed, the axis annotation of the tick at 
position 1 is left out because R thinks there is not enough space left.
You can workaround this point by making the label appear separately as 
in:
axis(side=1, at=c(0,3,5,7,10,14,21))
axis(1, 1)

Uwe Ligges