Closed Sneha-bioinfo closed 2 years ago
ivanek
commented
2 years ago Hi @Sneha-bioinfo, This is not an issue for GitHub. This should be discussed in the Bioc Mailing list. However this particular question is also mentioned in the Gviz vignette:
.... Or we can plot the union of all the exons in some sort of meta-transcript.
plotTracks(grtrack, collapseTranscripts = "meta", shape = "arrow",
transcriptAnnotation = "symbol")....
Best, Robert
Sneha-bioinfo
commented
2 years ago Noted, Thank you!
Regards, Sneha
On Tue, Aug 23, 2022, 15:29 Robert Ivánek @.***> wrote:
Hi @Sneha-bioinfo https://github.com/Sneha-bioinfo, This is not an issue for GitHub. This should be discussed in the Bioc Mailing list. However this particular question is also mentioned in the Gviz vignette https://www.bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.html#45_GeneRegionTrack :
.... Or we can plot the union of all the exons in some sort of meta-transcript.
plotTracks(grtrack, collapseTranscripts = "meta", shape = "arrow", transcriptAnnotation = "symbol")
....
Best, Robert
— Reply to this email directly, view it on GitHub https://github.com/ivanek/Gviz/issues/66#issuecomment-1223842893, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVBYX3NCU4R4KE4RXM52YK3V2SOJ3ANCNFSM57DK6V6Q . You are receiving this because you were mentioned.Message ID: @.***>
I'm trying to create a probe map showing probes mapped to the IKZF1 gene. Using the GeneRegion Track, I'm trying to plot just the gene with it's exons ( at the DNA level).... before even splicing occurs. However the final plot show's all the 22 transcripts of the gene. Is there any way to plot just the gene? These are the commands i used:- chr <- "chr7"
TxDb<-TxDb.Hsapiens.UCSC.hg38.knownGene
grtrack <- GeneRegionTrack(TxDb, chromosome="chr", start = 50304124, end = 50405101, shape= "arrow") This is the output i created :-
I'm trying to create something like this ( the image is from a publication)