[Bioc-sig-seq] Error while trying to xyplot. Perhaps a lattice problem.

[Deepayan Sarkar]

On Wed, Apr 29, 2009 at 2:47 PM,  <ig2ar-saf2 at yahoo.co.uk> wrote:
> Hi Deepayan,
>
> I had a partial victory with xyplot.
>
> Changing chromosome == "chr19" to chromosome == "chr19.fa" indeed fixed the problem.
>
> I can plot to my screen now doing
>
> xyplot(log(count) ~ nread | sample,
>        as(gdapply(E1, islandReadSummary), "data.frame"),
>        subset = (chromosome == "chr19.fa" & nread <= 40),
>        layout = c(1, 4), pch = 16, type = c("p", "g"))
>
> Its a very nice 4-paneled figure for control 1, control 2, treatment 1 and treatment 2.
>
> The not so successful story is when I try to plot to an eps file. I do
>
> postscript(file = fileOutputGraph,
>            horizontal=FALSE,
>            onefile=FALSE, # needed for EPS output. It is counterintuitive.
>            paper="letter",
>            #width=8.5, height=8.5/3,
>            width=6, height=8.5,
>            colormodel="rgb")
>
> xyplot(log(count) ~ nread | sample,
>        as(gdapply(E1, islandReadSummary), "data.frame"),
>        subset = (chromosome == "chr19.fa" & nread <= 40),
>        layout = c(1, 4), pch = 16, type = c("p", "g"))
>
> but the eps that is produced has a beheaded top panel and the figure becomes only black and white.

See ?trellis.device for the color issue.

Are you aware that you need to say

dev.off()

to complete writing your EPS/PDF/PNG files? Try that and let us know
if you see something useful.

-Deepayan