[BioC] ggplot2 error

[Steve Lianoglou]

Hi,

On Wed, Jan 29, 2014 at 12:07 AM, Alyaa Mahmoud <alyamahmoud at gmail.com> wrote:
> I also get this error when I simply use plot:
>
> plot (df[,1], df[,2])
> Error in plot.window(...) : infinite axis extents [GEPretty(-inf,inf,5)]

This is not really the right forum for this question, as it is more
related to base R than Bioc, but anyway:

You must have some weird elements in df[,1] and df[,2] ... and by
weird, I mean that there are things in there that plot can't plot. Try
to look at the data and see what's there.

Is the data stored in these columns numeric?
Are there infinite values?
Are there NaNs, NAs, etc?

Look at is.finite, is.nan, is.numeric to answer those questions.
Also looking at `range(df[,1])` (and df[,2]) as well as
`summary(df[,1])` (and df[,2]) could be helpful.

Trying to plot one axis against a "known good one" could be helpful.
For instance, assuming these columns are indeed numeric, to test
df[,1] you could just:

R> plot(df[,1])

and see if you get an error. Try the same for df[,2]

HTH,

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech