I am making a barplot using barplot2 from gplots where each bar
represents a specific tree species. I have formatted the species names
on the x-axis so that the genus name is above the species name and
have then rotated the labels 45 degrees to save room. This is my code:
>columncolor<-c("grey20", "grey20",
"grey20", "grey70", "grey70",
"grey70", "grey70", "grey70", "grey70")
>speciesnames<-c("Dialium\nguianensis", "Inga\nalba",
"Tachigali
\nversicolor", "Brosimum\nutile",
"Caryocar\ncostaricense", "Castilla
\ntunu", "Otoba\nnovagranatensis", "Pourouma\nbicolor",
"Socratea
\nexorrhiza")
>barplot2(meanapAprilactivity, names.arg=speciesnames,
col=columncolor, xlab="Species", ylab="Soil acid phosphatase
activity
(nmol/h/g)", ylim=c(0,1000), plot.ci=T, ci.l=apAprilminusordered,
ci.u=apAprilplusordered, cex.lab=1.5)#FinalGraphs>aPApril_Genus.pdf
>xvals<-barplot2(meanapAprilactivity, col=columncolor,
xlab="Species", ylab="Soil acid phosphatase activity
(nmol/h/g)",
ylim=c(0,1000), plot.ci=T, ci.l=apAprilminusordered,
ci.u=apAprilplusordered, cex.lab=1.5)#FinalGraphs>aPApril_Genus.pdf
>text(xvals,par("usr")[3]-1, srt=45, adj=0.5,labels=speciesnames,
xpd=T)
I have a few problems/questions:
1) The middle of the species names are placed at the bottom of the
bar, such that half of the label is in the figure.
2) There is too much of a space between the genus and species name
(e.g. between Dialium and guianensis for my first species)
3) Do I use cex.axis to change the font size of the labels and cex.lab
to change the font size of xlab and ylab?
I don't understand par() well enough to know what to change. I figured
changing the numbers after "usr" might help but I don't understand
what these numbers refer to and guess and check hasn't gotten me
anywhere.
Thanks,
Adrienne Keller
Graduate Student, College of Forestry
University of Montana
adrienne.keller at umontana.edu
(Phone) 651-485-5822
On Jun 21, 2011, at 4:29 PM, Adrienne Keller wrote:> I am making a barplot using barplot2 from gplots where each bar > represents a specific tree species. I have formatted the species > names on the x-axis so that the genus name is above the species name > and have then rotated the labels 45 degrees to save room. This is my > code: > > >columncolor<-c("grey20", "grey20", "grey20", "grey70", "grey70", > "grey70", "grey70", "grey70", "grey70") > >speciesnames<-c("Dialium\nguianensis", "Inga\nalba", "Tachigali > \nversicolor", "Brosimum\nutile", "Caryocar\ncostaricense", "Castilla > \ntunu", "Otoba\nnovagranatensis", "Pourouma\nbicolor", "Socratea > \nexorrhiza") > >barplot2(meanapAprilactivity, names.arg=speciesnames, > col=columncolor, xlab="Species", ylab="Soil acid phosphatase > activity (nmol/h/g)", ylim=c(0,1000), plot.ci=T, > ci.l=apAprilminusordered, ci.u=apAprilplusordered, > cex.lab=1.5)#FinalGraphs>aPApril_Genus.pdf... "object 'meanapAprilactivity' not found"> >xvals<-barplot2(meanapAprilactivity, col=columncolor, > xlab="Species", ylab="Soil acid phosphatase activity (nmol/h/g)", > ylim=c(0,1000), plot.ci=T, ci.l=apAprilminusordered, > ci.u=apAprilplusordered, cex.lab=1.5)#FinalGraphs>aPApril_Genus.pdf > >text(xvals,par("usr")[3]-1, srt=45, adj=0.5,labels=speciesnames, > xpd=T) > > I have a few problems/questions: > > 1) The middle of the species names are placed at the bottom of the > bar, such that half of the label is in the figure.Without any data that's a bit hard to reproduce. Use dput(meanapAprilactivity ) And _what_ were your goals, anyway?> > 2) There is too much of a space between the genus and species name > (e.g. between Dialium and guianensis for my first species)Ditto.> > 3) Do I use cex.axis to change the font size of the labels and > cex.lab to change the font size of xlab and ylab?If you are referring to the text() call then cex will change the font size of the labels.> > I don't understand par() well enough to know what to change. I > figured changing the numbers after "usr" might help but I don't > understand what these numbers refer to and guess and check hasn't > gotten me anywhere.The third value of par("usr") is the min y value (in the natural units of the y variable) for the plot area, so if you were trying to place the text near the bottom of the plotted region, then subtracting 1 from it to get your y-text argument _might_ work, but if the range of y values is large you may overlap the lower border. Please describe your goals, rather than relying on code that doesn't give the desired result. mp <- barplot2(VADeaths) # default dimnames(VADeaths)[[2]] # [1] "Rural Male" "Rural Female" "Urban Male" "Urban Female" speciesnames <-c("Rural\nMale" , "Rural\nFemale","Urban\nMale" , "Urban\nFemale") # increasing the value subtracted from y1 lowers the position of the labels xvals<-barplot2(VADeaths); text(xvals,par("usr")[3]-8, srt=45, adj=0.5,labels=speciesnames, xpd=T)> > Thanks, > > > Adrienne Keller > Graduate Student, College of Forestry > University of Montana > adrienne.keller at umontana.edu > (Phone) 651-485-5822 > > ______________________________________________ > R-help at r-project.org 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.David Winsemius, MD West Hartford, CT
You might try: text(xvals,-50,labels=speciesnames,cex=.7,xpd=T) You can also make the plot wider. There are a number of ways to do this. For example (on a mac): quartz(width=10,height=6) or simply stretch it On Tue, Jun 21, 2011 at 4:29 PM, Adrienne Keller <adrienne.keller at gmail.com> wrote:> I am making a barplot using barplot2 from gplots where each bar represents a > specific tree species. I have formatted the species names on the x-axis so > that the genus name is above the species name and have then rotated the > labels 45 degrees to save room. This is my code: > >>columncolor<-c("grey20", "grey20", "grey20", "grey70", "grey70", "grey70", >> "grey70", "grey70", "grey70") >>speciesnames<-c("Dialium\nguianensis", "Inga\nalba", >> "Tachigali\nversicolor", "Brosimum\nutile", "Caryocar\ncostaricense", >> "Castilla\ntunu", "Otoba\nnovagranatensis", "Pourouma\nbicolor", >> "Socratea\nexorrhiza") >>barplot2(meanapAprilactivity, names.arg=speciesnames, col=columncolor, >> xlab="Species", ylab="Soil acid phosphatase activity (nmol/h/g)", >> ylim=c(0,1000), plot.ci=T, ci.l=apAprilminusordered, >> ci.u=apAprilplusordered, cex.lab=1.5)#FinalGraphs>aPApril_Genus.pdf >>xvals<-barplot2(meanapAprilactivity, col=columncolor, xlab="Species", >> ylab="Soil acid phosphatase activity (nmol/h/g)", ylim=c(0,1000), plot.ci=T, >> ci.l=apAprilminusordered, ci.u=apAprilplusordered, >> cex.lab=1.5)#FinalGraphs>aPApril_Genus.pdf >>text(xvals,par("usr")[3]-1, srt=45, adj=0.5,labels=speciesnames, xpd=T) > > I have a few problems/questions: > > 1) The middle of the species names are placed at the bottom of the bar, such > that half of the label is in the figure. > > 2) There is too much of a space between the genus and species name (e.g. > between Dialium and guianensis for my first species) > > 3) Do I use cex.axis to change the font size of the labels and cex.lab to > change the font size of xlab and ylab? > > I don't understand par() well enough to know what to change. I figured > changing the numbers after "usr" might help but I don't understand what > these numbers refer to and guess and check hasn't gotten me anywhere. > > Thanks, > > > Adrienne Keller > Graduate Student, College of Forestry > University of Montana > adrienne.keller at umontana.edu > (Phone) 651-485-5822 > > ______________________________________________ > R-help at r-project.org 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. >