Question: Nice plot of gene region (plotTracks function)
0
2.7 years ago by
Poland

Hello

I trying to make a nice plot such as in here:

https://bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.pdf

I mean, chromosome at the top and gene (I need only one gene) below, exons presetned as blocks and introns as line with arrows.

My plot looks like this:

and my code:

library(org.Hs.eg.db)
eid <- select(org.Hs.eg.db, "GNG7", "ENTREZID", "SYMBOL")[["ENTREZID"]]
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
txid <- select(txdb, eid, "TXNAME", "GENEID")[["TXNAME"]]
exons <- exonsBy(txdb, by="tx", use.names=TRUE)
gng7exons <- exons[names(exons) %in% txid]
gng7exons[[1]]
anno <- AnnotationTrack(gng7exons)
plotTracks(list(gtrack,itrack,anno), from = 2645916, to = 2646703, cex = 0.8)

It is even possible to add SNP's, cpg islands, etc to this plot? Summarizing, I'm looking for something like in UCSC and I have no idea how to get it...

gviz granges plottracks • 579 views
modified 2.7 years ago • written 2.7 years ago by Adam0

There are dozens of plots in the Gviz User's Guide, so pointing to the entire document as an example isn't particularly helpful. In addition, the code to generate all the plots in that guide are there as well, so if you like a particular plot, is it not possible to emulate the accompanying code?

There are also examples of adding CpG islands and SNPs, along with the code to do that. Is there something in particular about the guide that you don't understand?

I get what I want finally, but I won't put it here. This page isn't for help others, is it?