R help - Oct 2012 - Navigating a grid.

Greetings

I am trying to make a multiple panel plot 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 pop/push/down/seekViewport commands at the end of  
the plotpush method. There must be something I'm missing in the  
documentation, I believe what I have should work. I haven't been able  
to find a similar scenario in the help archives.

Could I get someone to critique my code and help me figure out how to  
make multiple plots in columns and rows?

Thanks

Mike

plotpush <- function(x,n,letter,row,column) {
      
pushViewport 
(viewport 
(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"
     )
     popViewport(0)
}

pushViewport(viewport(layout = grid.layout(nrow=26,ncol=2)))

sapply(repeats,plotpush,n=1:26,letter=1:26,row=1:26,col=1)
sapply(repeats,plotpush,n=27:52,letter=1:26,row=1:26,col=2)

 > 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
 >

Sent from my iPhone

Begin forwarded message:
> From: Michael Muratet <muratetm@gmail.com>
> Date: October 21, 2012 12:08:55 PM CDT
> To: r-help@r-project.org
> Subject: Navigating a grid.
> 
> Greetings
> 
> I am trying to make a multiple panel plot 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
pop/push/down/seekViewport commands at the end of the plotpush method. There
must be something I'm missing in the documentation, I believe what I have
should work. I haven't been able to find a similar scenario in the help
archives.
> 
> Could I get someone to critique my code and help me figure out how to make
multiple plots in columns and rows?
> 
> Thanks
> 
> Mike
> 
> plotpush <- function(x,n,letter,row,column) {
>   
pushViewport(viewport(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"
>    )
>    popViewport(0)
> }
> 
> pushViewport(viewport(layout = grid.layout(nrow=26,ncol=2)))
> 
> sapply(repeats,plotpush,n=1:26,letter=1:26,row=1:26,col=1)
> sapply(repeats,plotpush,n=27:52,letter=1:26,row=1:26,col=2)
> 
> > 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
> >
	[[alternative HTML version deleted]]