[R] plot - no main title and missing abscissa value

[Uwe Ligges]

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