Re: [R-sig-eco] question for the R community : Plot RDA biplot without axis ?
Hi :D
I finally had the chance to try your solutions. It was fast to modify
the code of the function and it worked!
I really appreciate your comments and your help. You are fast and clear !
I modified my code and I will never put white axes ever again ;)
Thank you very much.
2013/2/26 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
>>
>>> 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 ax
Re: [R-sig-eco] question for the R community : Plot RDA biplot without axis ?
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
>
>> 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 ide
Re: [R-sig-eco] question for the R community : Plot RDA biplot without axis ?
Sarah, We indeed insist on drawing scale of arrows for text() and point() function of cca/rda/capscale. Currently the only way to avoid this is to edit the function. I'll see what to do with this. One piece of advice: do not use col.axis = "white" which will draw white axes. The background of the graph is transparent but the plot is displayed on white canvas so that you cannot see white axes. The white axes are still, like you will see if you look at the graph against some other colour (which happens most easily if you copy the graph and display it in slides or in a poster with coloured background). The canonical way is to suppress axes: plot(dune.cca, type="n", scaling = 2, axes = FALSE, xlab = "", ylab = "") Here 'axes' suppress drawing axes and to be sure, xlab and ylab use zero-length strings "" so that axis labels are also suppressed. You can later use box() to frame the empty graph if needed. 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 > >> 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 lin
Re: [R-sig-eco] question for the R community : Plot RDA biplot without axis ?
Hi Sarah,
Here is Gavin's solution.
You have to modify the text.cca function. (at least) two ways:
# First
#without paranthèses after function name, you get the source codes
vegan:::text.cca
#then copy/paste this source codes, modify, save, and assign name space
#Second
# you can modify directly the function using fixInNamespace()
fixInNamespace("text.cca",ns="vegan") #this function opens a script editor
(in RStudio, I don't know in other config), you have to remove/modify lines
32 to 35.
#then you just have to run your codes, but just precise in your calls
"vegan:::text.cca" instead" of "text".
### 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
vegan:::text.cca(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))
vegan:::text.cca(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))
vegan:::text.cca(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))
vegan:::text.cca(dune.cca, display="bp", col=1, cex=1.1)
I hope it helps
Pierre
2013/2/26 Sarah Loboda
> 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
>
> > 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 th
Re: [R-sig-eco] question for the R community : Plot RDA biplot without axis ?
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 > 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]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] question for the R community : Plot RDA biplot without axis ?
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 > ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
[R-sig-eco] question for the R community : Plot RDA biplot without axis ?
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. 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]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
