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@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/*

	[[alternative HTML version deleted]]

