[R-sig-eco] question for the R community : Plot RDA biplot without axis ?

[Jari Oksanen]

Sarah,

I added argument 'axis.bp' to text.cca and points.cca functions. To upgraded functions can be found in http://vegan.r-forge.r-project.org/ (rev2452), and will probably be included in the next minor release of vegan (2.0-7) scheduled for March, 2013.

You can also get the single files from R-Forge, or you can install devel version of vegan with

install.packages("vegan", repos="http://r-forge.r-project.org")

It will take a day at minimum to get the version packaged in R-Forge.

Cheers, Jari Oksanen

On 26 Feb 2013, at 3:49, Sarah Loboda wrote:

> Hi,
> Here's the reproducible example that I made with dune data. When you do the
> 4 graphs, you can see that because of the text () function, there is an
> axis on the right and values appear in the plots on the right side. I
> understand that it is because of my text () function, but is there a way to
> delete that axis in the text funtion? if not, is there another way to plot
> my data on 4 panels without axis?
> 
> I don't know what you mean by "body of vegan text.cca". You mean in the
> vegan tutorial ?
> I used col.axis because ann=FALSE as an argument in plot function does not
> work and col.axis seems fine...
> 
> Thank you very much for your time. I really appreciate your help :D
> 
> library(vegan)
> library(MASS)
> 
> ### data
> data(dune)
> data(dune.env)
> 
> ### Constrained ordination
> dune.hel<-decostand(dune, "hellinger")
> dune.cca <- cca(dune ~ A1 + Manure, data=dune.env)
> 
> ### Plot with 4 panels
> par(mfrow=c(2,2))
> par(mar=c(0.3,0.3,0.3,0.3))
> 
> 
> ### plot 1
> plot(dune.cca, type = "n", scaling = 2, col.axis="white")
> with(dune.env, points(dune.cca, display = "sites", scaling = 2, cex=1.3,
> col=2))
> ### When I add the next line, it adds env. variables as arrows but also
> adds an axis on the right
> text(dune.cca, display="bp", col=1, cex=1.1)
> 
> ###plot 2
> plot(dune.cca, type = "n", scaling = 2, col.axis="white", col="grey")
> with(dune.env, points(dune.cca, display = "sites", scaling = 2, cex=1.3,
> col=2))
> text(dune.cca, display="bp", col=1, cex=1.1)
> 
> ###plot 3
> plot(dune.cca, type = "n", scaling = 2, col.axis="white")
> with(dune.env, points(dune.cca, display = "sites", scaling = 2, cex=1.3,
> col=2))
> text(dune.cca, display="bp", col=1, cex=1.1)
> 
> ###plot 4
> plot(dune.cca, type = "n", scaling = 2, col.axis="white")
> with(dune.env, points(dune.cca, display = "sites", scaling = 2, cex=1.3,
> col=2))
> text(dune.cca, display="bp", col=1, cex=1.1)
> 
> 2013/2/25 Gavin Simpson <gavin.simpson at ucl.ac.uk>
> 
>> On Mon, 2013-02-25 at 13:18 -0500, Sarah Loboda wrote:
>>> Hi,
>>> I have trouble to obtain the ordination graph I want. I want to have 4
>> RDA
>>> biplot on the same page and I don't want to have (or I want to modify)
>> the
>>> axis numbers. I want the marks on the axis without numbers to maximize
>> the
>>> space for each RDA plot.
>> 
>> A problem is the call to text() ( which calls text.cca() ). It doesn't
>> pass on arguments to the underlying axis() calls and hence you can't do
>> what you are trying to do with that function directly.
>> 
>> Not sure why you want the axis to be white - that draws an axis so it
>> will obscure anything drawn before it with white paint.
>> 
>> The only solution at the moment will be to modify the vegan:::text.cca()
>> function to change the two calls to axis() at the end of the function
>> definition. I suspect you could just copy the body of vegan:::text.cca
>> and put it into your own function, but I haven't tried it. If that fails
>> due to namespace issues, then use assignInNamespace() to assign your
>> function to the text.cca function in vegans namespace.
>> 
>> See the relevant help pages on how to do this. I'm about to leave the
>> office so I can't help further now, but if you have trouble email back
>> to the list and I'll see about cooking up and example...
>> 
>> All the best
>> 
>> Gavin
>> 
>>> This seems like a simple task but I tried different approaches and
>> coudn't
>>> figure out how to change my axis. This is my code :
>>> 
>>> par(mfrow=c(2,2))
>>> par(mar=c(0.2,0.2,0.2,0.2))
>>> 
>>> ### first RDA biplot
>>> with(arctic, levels(site))
>>> shapevec<- c(19,19,19,19,19,19,19,19,19,19,19,19,6,6,6,6,6,6,6,6,6,6,6,6)
>>> plot(spiders.rda.a, type = "n", scaling = 2, las=1, tcl=0.2,
>>> col.axis="white")
>>> with(spiders.env.a, points(spiders.rda.a, display = "sites",
>>>                                scaling = 2, pch = shapevec, cex=1.3))
>>> text(spiders.rda.a, display="bp", cex=1.1, col.axis="white", ann=FALSE)
>>> #### it is when I run this line that my y axis appear on the right but I
>>> don't want to
>>> ### in yellow, this is what I tried to make it diseappear. To put those
>>> arguments in plot() doesn't change anything.
>>> 
>>> What should I had in the text part to make sure that the axis doesn't
>> show
>>> up?
>>> My intention is to plot my sites as dots without text and my arrows for
>>> environmental variables with the name of each variable. Any other ideas
>> on
>>> rda plot will be greatly appreciated.
>>> Thank you very much :D
>>> 
>> 
>> 
>> 
>> 
> 
> 
> -- 
> Sarah Loboda
> MSc candidate, Entomology,
> Department of Natural Resource Sciences
> McGill University
> *http://insectecology.mcgill.ca/*
> 
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> 
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