Dear Dr. Murrell
Sorry to bother you at home, so to speak, but my emails to r-help at
r-project.org
are falling into the void.
I am trying to make a multiple panel plot with 26 rows and 2 columns
with plots from a tool (genoPlotR) that is layered on grid. My code
and session info are below. When I execute the code, I get a single
plot in the center of the graphics page. I have tried various viewport
and pop/push/down/seekViewport commands. There must be something I'm
missing in the documentation, I believe what I have should work. I
have been able to find a few similar scenarios in the help archives
but enlightenment eludes me.
Could I get you to critique my latest version of the code below and
help me figure out how to combine multiple plots in columns and rows?
The code below produces a graphic with all the plots overlaid on the
left middle side of the graphics window. And I get the following
warnings repeated 50 times:
> warnings()
Warning messages:
1: In while (!rootVP(pvp)) { ... :
the condition has length > 1 and only the first element will be used
plotpush <- function(x,n,letter,row,column,layout) {
pushViewport
(viewport
(layout
=gl,layout.pos.row=row,layout.pos.col=column,name=as.character(n)))
plot_gene_map
(dna_segs=list(x[["seg"]]),annotations=x[["annot"]],dna_seg_scale=T,
scale_cex
=
1.4
,dna_seg_line
=F,plot_new=FALSE,scale=F,arrow_head_length=1,annotation_cex=1.4,
main=toupper(letters[n]),main_pos="left"
)
}
gl <- grid.layout(nrow=26,ncol=2)
pushViewport(viewport(layout = gl)
segs <- c(segs.cys.115,segs.cys.196,segs.asp.388,segs.asp.1060,segs.gly)
sapply(segs,plotpush,n=1:26,letter=1:26,row=1:26,column=1,layout=gl)
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets
methods base
other attached packages:
[1] GenomicFeatures_1.9.41 AnnotationDbi_1.19.38
Biobase_2.17.8 GenomicRanges_1.9.65 IRanges_1.15.44
BiocGenerics_0.3.2
[7] genoPlotR_0.8 ade4_1.4-17
loaded via a namespace (and not attached):
[1] biomaRt_2.13.2 Biostrings_2.25.12 bitops_1.0-4.1
BSgenome_1.25.8 DBI_0.2-5 RCurl_1.91-1
[7] Rsamtools_1.9.30 RSQLite_0.11.2 rtracklayer_1.17.19
stats4_2.15.0 tools_2.15.0 XML_3.9-4
[13] zlibbioc_1.3.0
>
Thanks
Mike
Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)
Room 4005
601 Genome Way
Huntsville, Alabama 35806
