[BioC] pdmClass plot error

[Dick Beyer]

Hi Jim,

I am using the pdmclass package and had a question.  I'd like to be able to plot the output from pdmClass when there are only 2 levels.  However, that generates an error.

Here is the example from the pdf documentation with a change to show the problem:

library("pdmclass")
data("fibroEset")
y <- as.factor(pData(fibroEset)[, 2])
x <- t(exprs(fibroEset))
gn.class <- pdmClass(y ~ x, method = "pls")
plot(gn.class, pch = levels(y))

Now change the levels of y so there are only two:

y <- as.character(pData(fibroEset)[, 2])
> y
  [1] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" "g" "g" "g" "g" "g" "g" "g" "g" "g" "g" "g" "g" "h" "h" "h" "h" "h" "h" "h" "h" "h" "h" "h" "h" "h"
[37] "h" "h" "h" "h" "h" "h" "h" "h" "h" "h"
y[y=="g"] <- "b"
y <- as.factor(y)
y
  [1] b b b b b b b b b b b b b b b b b b b b b b b h h h h h h h h h h h h h h h h h h h h h h h
Levels: b h

gn.class <- pdmClass(y ~ x, method = "pls")
plot(gn.class, pch = levels(y))
Error in rbind(vars[, coord.pair], means[, coord.pair]) :
   subscript out of bounds
predict(gn.class)
  [1] b b b b b b b b b b b b b b b b b b b b b b b h h h h h h h h h h h h h h h h h h h h h h h
Levels: b h

I've poked around the mda:::plot.fda function and I can see why I get an error.  But I was wondering, given predict still works with 2 levels, how to plot the predictions?

Thanks much,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
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 			Seattle, WA 98105-6099
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http://staff.washington.edu/~dbeyer
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