
Thanks steffen, I will try your suggestions. > Date: Tue, 25 Nov 2008 20:51:21 -0800> Subject: Re: [BioC] Using GenomeGraphs effectively for generating publication quality pictures> From: steffen@stat.Berkeley.EDU> To: daren76@hotmail.com> CC: bioconductor@stat.math.ethz.ch> > Hi Daren,> > > 1) How to include the cytoband information e.g. 4q to the ideogram ? How> > to label the gene in the cytoband with "IL8" ?> > Currently you can not include cytoband information on the ideogram. How> would you want this to look like?> > > 2) What colour is actually used by gene and transcript ? I have created a> > legend with "orange" and "lightblue", but the colour doesn't look the> > same.> > You can set your own colors for these by the DisplayPars function when> creating genes and transcripts, e.g.:> > gene <- new("Gene", id = "TP53", type="hgnc_symbol", biomart = mart,> dp=DisplayPars(color="green"))> > > By default the colors are orange for genes and cornflowerblue for> transcripts.> > > 3) How to make the legend a single line ? Currently, the words are below> > the boxes> > This is hard-coded at this point.> > > 4) I have affy U133A, exon 1.0ST and agilent 44K probes to map to the> > gene. How can I do that ?> > I think all these platforms are in Ensembl so you could use biomaRt to> link them to the Ensembl Gene id. Here's an example:> > library(biomaRt)> mart = useMart("ensembl", dataset="hsapiens_gene_ensembl")> map = getBM(c("ensembl_gene_id", "affy_hg_u133a"), filters => "affy_hg_u133a", values=c("209718_at","221633_at"), mart=mart)> > >map> ensembl_gene_id affy_hg_u133a> 1 ENSG00000025770 209718_at> 2 ENSG00000025770 221633_at> > > > 5) How to space the numbers away from the genomeAxis so that it looks less> > clustered ?> > This is hard-coded at this time as well.> > Hope this helps.> Steffen> > >> > Hi,> >> > I am using GenomeGraphs to generate gene structures. My codes are below:> >> > A few questions that I have> > 1) How to include the cytoband information e.g. 4q to the ideogram ? How> > to label the gene in 
the cytoband with "IL8" ?> > 2) What colour is actually used by gene and transcript ? I have created a> > legend with "orange" and "lightblue", but the colour doesn't look the> > same.> > 3) How to make the legend a single line ? Currently, the words are below> > the boxes> > 4) I have affy U133A, exon 1.0ST and agilent 44K probes to map to the> > gene. How can I do that ?> > 5) How to space the numbers away from the genomeAxis so that it looks less> > clustered ?> >> >> > library("biomaRt")> > library("GenomeGraphs")> >> > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")> > drawGS <- function(gene_symbol) {> > gs <- getBM(attributes=c("hgnc_symbol", "ensembl_gene_id",> > "chromosome_name", "start_position", "end_position", "band"),> > filter=c("hgnc_symbol"), values=gene_symbol, mart=mart)> >> > title <- new("Title", title = paste(gs[1], ":", gs[2]), dp => > DisplayPars(color = "darkred"))> > ideog <- new("Ideogram", chromosome = as.character(gs[3]))> > genomeAxis <- new("GenomeAxis", add53 = TRUE, add35 = TRUE)> > gene <- new("Gene", id = as.character(gs[2]), biomart = mart)> > transcript <- new("Transcript", id = as.character(gs[2]), biomart => > mart)> >> > legend <- new("Legend", legend = c("gene", "transcript"), dp => > DisplayPars(color = c("orange", "lightblue")))> >> > pdf(paste(gene_symbol, ".pdf", sep=""))> > gdPlot(list(title, ideog, genomeAxis, gene, transcript, legend), minBase> > = as.integer(gs[4]), maxBase = as.integer(gs[5]))> > dev.off()> > }> >> > drawGS("IL8")> > _________________________________________________________________> > [[elided Hotmail spam]]> >> > _______________________________________________> > Bioconductor mailing list> > Bioconductor@stat.math.ethz.ch> > https://stat.ethz.ch/mailman/listinfo/bioconductor> > Search the archives:> > http://news.gmane.org/gmane.science.biology.informatics.conductor> >> 
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