Question: Using GenomeGraphs effectively for generating publication quality pictures
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gravatar for Daren Tan
10.7 years ago by
Daren Tan160
Daren Tan160 wrote:
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]]
ADD COMMENTlink modified 10.6 years ago by steffen@stat.Berkeley.EDU600 • written 10.7 years ago by Daren Tan160
Answer: Using GenomeGraphs effectively for generating publication quality pictures
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gravatar for steffen@stat.Berkeley.EDU
10.6 years ago by
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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 10.6 years ago by steffen@stat.Berkeley.EDU600
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> >> _________________________________________________________________ [[alternative HTML version deleted]]
ADD REPLYlink written 10.6 years ago by Daren Tan160
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