[BioC] GenomeGraph

라벨: Informatics
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http://www.alexaplatform.org/examples/GenomeGraphsExample.R

#GenomeGraphs example
#This example was tested with R2.14.1

#Install package if you have not already done so
source("http://bioconductor.org/biocLite.R")
biocLite("GenomeGraphs")

#Load libraries 
library(GenomeGraphs)

#Draw the gene and then just one specific transcript of that gene
mart = useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
gene = makeGene(id = "ENSG00000171988",type = "ensembl_gene_id", biomart = mart)
transcript = makeTranscript(id = "ENST00000399262", type="ensembl_transcript_id", biomart = mart)
gdPlot(list(gene, transcript))

#Draw the gene and then all transcripts of that gene
gene = makeGene(id = "ENSG00000171988",type = "ensembl_gene_id", biomart = mart)
transcript = makeTranscript(id = "ENSG00000171988", type="ensembl_gene_id", biomart = mart)
gdPlot(list(gene, transcript))

#Draw a more annotated figure (using the gene UMPS as an example)
gene = makeGene(id = "ENSG00000114491",type = "ensembl_gene_id", biomart = mart)
transcript = makeTranscript(id = "ENSG00000114491", type="ensembl_gene_id", biomart = mart, dp=DisplayPars(plotId=TRUE, cex=0.5))

#Create an ideogram for the entire chromosome 3
ideog = new("Ideogram", chromosome = "3")

#Create a highlight of the gene position on the ideogram using "absolute coordinates" 
ol1 = makeRectangleOverlay(0.60, 0.65, region=c(0.75, 0.82), coords ="absolute", dp = DisplayPars(alpha = .2, fill = "red"))

#Create a highlight of exon 2 of UMPS spanning across the gene and transcript tracks
ol2 = makeRectangleOverlay(124453840, 124454200, region=c(3,4), coords = c("genomic", "absolute"), dp = DisplayPars(alpha = .2, fill = "olivedrab1"))

#Create the plot
gdPlot(list(makeTitle("UMPS"), "Chr3"=ideog, "Gene"=gene, "Transcripts"=transcript), overlays=list(ol1,ol2))

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라벨: Informatics