[R] Plotting two distance matrices

[Jari Oksanen]

> 
> I'm trying to plot two distance matrices against each other
> (74x74,phylogenetic distance and phenotypic distances). However R
> gives an error message:"Error in plot.new() : figure margins too
> large".
> 
> Is it because I have too many points to plot?

No. It *sounds* like you don't have distance matrices but data frames of
distances, because this is the error message that you get. The default
plot of a data frame is a pairs() plot of all columns (variables)
against each other. You will have a data frame if you read in your
distances from an external file (or changed them into data frame). Try
changing your data sets into regular R dist objects, and plot these
against each other (and as.dist really seems to work to data frames
directly):

plot(as.dist(d1), as.dist(d2))

This was only guessing, since the message did not contain sufficient
information.

cheers, jari oksanen