R help - Jan 2010 - ordisymbol - changing symbols used in plotting factor levels

Hello,

I'm trying plot points in an NMDS according to a factor with two levels:

fig<-ordiplot(canod.sol,  
type="none",cex.axis=0.9,cex.lab=0.1,pty="m",tck=-0.01)
ordisymbol(fig, y = hab, factor = "habitat", rainbow = T,col = env,  
legend = F)

This gets me part of the way - It produces a plot with blue triangles  
for the first factor level and red circles for the second level. What  
I want to do is change the symbols so they all plot as circles, then  
change the colours used to plot each factor level (e.g. I want blue  
circles and red circles). Any advice on how to do this?

Thanks,
Colin Curry
--
Colin Curry
Ph.D. Candidate
Canadian Rivers Institute
Department of Biology
University of New Brunswick, Fredericton


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On Tue, 2010-01-26 at 19:59 -0400, Colin Curry wrote:
> Hello,
> 
> I'm trying plot points in an NMDS according to a factor with two
levels:
> 
> fig<-ordiplot(canod.sol,  
> type="none",cex.axis=0.9,cex.lab=0.1,pty="m",tck=-0.01)
> ordisymbol(fig, y = hab, factor = "habitat", rainbow = T,col =
env,
> legend = F)
> 
> This gets me part of the way - It produces a plot with blue triangles  
> for the first factor level and red circles for the second level. What  
> I want to do is change the symbols so they all plot as circles, then  
> change the colours used to plot each factor level (e.g. I want blue  
> circles and red circles). Any advice on how to do this?
You can't, not with the way that function is currently implemented. It
would have helped if you'd told us that this was in BiodiversityR ---
originally I thought it was in vegan.

You have to hack the code yourself. The example below, I think, will now
do what you want:

`Myordisymbol` <-
function(ordiplot,y,factor,col=1,rainbow=T,legend=T,...) {
    ordiscores <- scores(ordiplot, display="sites")
    groups <- table(y[,factor])
    m <- length(groups)
    if (m > 25) {
        warning("Symbol size was kept constant as there were more than 25
categories (> number of symbols that are currently used in R)")
        rainbow <- T
    }
    levels <- names(groups)
    if (rainbow == T) {palette(rainbow(m))}
    for (i in 1:m) {
        subs <- y[,factor]==levels[i]
        for (q in 1:length(subs)) {
            if(is.na(subs[q])) {subs[q]<-F}
        }
        scores <- ordiscores[subs,,drop=F]
        if (rainbow == T && m < 26) {
            ## Keep plotting char same for all groups
            ##points(scores[,1],scores[,2],pch=i,col=i,...)
            points(scores[,1],scores[,2],pch=1,col=i,...)
        }
        if (rainbow == T && m > 25) {
            points(scores[,1],scores[,2],pch=19,col=i,...)
        }
        if (rainbow == F) {
            ## Keep plotting char same for all groups
            ##points(scores[,1],scores[,2],pch=i,col=col,...)
            points(scores[,1],scores[,2],pch=1,col=col,...)
        }
    }
    if (legend==T) {
        if (rainbow==T && m<26)
{legend(locator(1),legend=levels,pch=c(1:m),col=c(1:m))}
        if (rainbow==T && m>25)
{legend(locator(1),legend=levels,pch=rep(19,m),col=c(1:m))}
        if (rainbow==F) {legend(locator(1),legend=levels,pch=c(1:m))}
    }
    palette("default")
}

But that isn't using your (nor was it ever if the call you show above is
correct) setting of 'col' to 'env'. As you have rainbow = TRUE
and m
*is* < 26 (m == 2 in your case), the colour used to plot is colour i
{1,...,m} using the rainbow palette.

Anyway, HTH

G
> 
> Thanks,
> Colin Curry
> --
> Colin Curry
> Ph.D. Candidate
> Canadian Rivers Institute
> Department of Biology
> University of New Brunswick, Fredericton
> 
> 
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> 
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