[BioC] Genome Graphs question

[Wolfgang Huber]

Hi Paul

this is because GenomeGraphs uses "grid" graphics. The grid graphics 
system is much more flexible and more consistently designed than R's 
traditional graphics, and the two do not mix.

Have a look into the excellent book
"R Graphics" by Paul Murrell, published by Chapman & Hall
http://www.amazon.co.uk/Graphics-Computer-Science-Data-Analysis/dp/158488486X

	Best wishes
	Wolfgang

Paul Leo ha scritto:
> So have genomeGraphs making plots I need. BUT have come to a catch; I
> want to add the genomeGraph plots as part of other plots using the
> typical layout() command. However the genomeGraphs "plot" command
> gdPlot() writes a new plot when it is called, or overwrites layout .
> Can't find options to fix. 
> 
> For example in below I would like to make a plot of x vs X^2 above a
> genome graphs plot but this fails:
> 
> 
> ########## get goodies for genome graphs
> library(GenomeGraphs)
> mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
> minStrand <- makeGeneRegion(chromosome = 17,start = 30450000, end =
> 30550000,strand = "-", biomart = mart)
> ideogram <- makeIdeogram(chromosome = 17)
> genomeAxis <- makeGenomeAxis(add53 = TRUE,add35 = TRUE)
> ####################
> 
> nf <- layout(matrix(c(1,2), byrow=TRUE))
> layout.show(nf)
> x<-1:100
> y<-x^2
> plot(x,y)
> gdPlot(list(ideogram, plusStrand, genomeAxis, minStrand), minBase =
> 30450000, maxBase = 30550000)
> 
> 
>> sessionInfo()
> R version 2.9.0 (2009-04-17) 
> x86_64-pc-linux-gnu 
> 
> locale:
> LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets
> methods  
> [8] base     
> 
> other attached packages:
> [1] GenomeGraphs_1.4.0 biomaRt_2.0.0     
> 
> loaded via a namespace (and not attached):
> [1] lattice_0.17-22 RCurl_0.94-1    tools_2.9.0     XML_1.95-3
> 
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-- 

Best wishes
      Wolfgang

------------------------------------------------
Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber