Hi everybody,

Is there a way of changing the default parameters of the plots crated by the
simpleaffy packge - pairwise.comparison plots.

I want to plot two data aets on the same plot, but they all have the same
three colors (red, orange and yellow). I tried to assign them different
colours but I always get an error message, that I have multiple allocations
for the same parameters.
The same happens when I tried to set new titles for my X- and Y-axis.

This is how I tried it:

> plot(significant.rma_w,type="scatter") #scatter plot> plot(significant.rma_d,type="scatter", col = c("purple","blue","green"), add=T) #scatter plotError in plot.xy(xy.coords(x, y), type = type, ...) :
  formal argument "col" matched by multiple actual arguments

I get a similar error message when trying to set new captions for the axes.

> plot(results.rma_w,significant.rma_w, type="scatter",+ main= "significantly deregulated genes between high and low fractions",+ xlab="high density fraction (w)", ylab ="low density fraction (w)" ) #scatter plotError in plot.default(x, y, xlim = xlim, ylim = ylim, pch = pch, ...) :
  formal argument "xlab" matched by multiple actual arguments

when doing plot.pairwise.comparison.plot I get only this:

> plot.pairwise.comparisonfunction (x, y = NULL, labels = colnames(means(x)), showPMA = TRUE,
    type = "scatter", ...)
{
    if (type == "scatter") {
        .pcscatterplot(x, y, labels, showPMA, ...)
    }
    else if (type == "volcano") {
        .volcanoplot(x, y, labels, showPMA, ...)
    }
    else if (type == "ma") {
        .maplot(x, y, labels, showPMA, ...)
    }
}
<environment: namespace:simpleaffy>


But when looking for, there is no such real functions to work with as
.pcscatterplot.


I will appreciate any kind of helps

THX

Assa

> R.Version()$platform
[1] "x86_64-pc-linux-gnu"

$arch
[1] "x86_64"

$os
[1] "linux-gnu"

$system
[1] "x86_64, linux-gnu"

$status
[1] ""

$major
[1] "2"

$minor
[1] "12.2"

$year
[1] "2011"

$month
[1] "02"

$day
[1] "25"

$`svn rev`
[1] "54585"

$language
[1] "R"

$version.string
[1] "R version 2.12.2 (2011-02-25)"

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