Question

gviz library plot 2 gene loci in the same figure

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tangming2005 ▴ 200

@tangming2005-6754

Last seen 4 months ago

United States

I want to plot two different gene loci using GeneRegionTrack() function in the same figure. It is not allowed looks like

grtrack2 <- GeneRegionTrack(txdb, chromosome = "chr6", 
                            start = 35995000, end = 40000000)

grtrack3<- GeneRegionTrack(txdb, chromosome = "chr7",
                           start = 35005000, end = 40000000)

plotTracks(list(grtrack2, grtrack3)

Warning message:
In plotTracks(list(grtrack2, grtrack3)) :
The track chromosomes in 'trackList' differ. Setting all tracks to chromosome 'chr6'

How can I get around with it? In addition, how can I only plot one transcript from the txdb rather than all of them?

Thanks!

Ming Tang

gviz • 1.7k views

ADD COMMENT • link updated 9.4 years ago by florian.hahne@novartis.com ★ 1.6k • written 9.5 years ago by tangming2005 ▴ 200

score 0 · Answer 1 · 2015-08-20

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florian.hahne@novartis.com ★ 1.6k

@florianhahnenovartiscom-3784

Last seen 6.4 years ago

Switzerland

Hi Ming,

I'd suggest you take a closer look at the package vignette. In particular Chapter 2 highlights the basic ideas behind the package. Chapter 6 has some suggestions for multiple chromosome plots.

Florian

ADD COMMENT • link 9.5 years ago florian.hahne@novartis.com ★ 1.6k

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Thanks Florian for the comments. I am just getting familiar with the package and have just finished reading the tutorial.

One problem I have is that the chromosome name naming conventions between ucsc and Ensemble. If I want to plot a Ideogram from UCSC and a biomart gene track together, I always have the warning that the chr name is different between tracks.

Anyway to get around with it?

Thanks,

Ming

ADD REPLY • link 9.5 years ago tangming2005 ▴ 200

score 0 · Answer 2 · 2015-08-31

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florian.hahne@novartis.com ★ 1.6k

@florianhahnenovartiscom-3784

Last seen 6.4 years ago

Switzerland

Hm, this should not happen. When fetching data from Biomart, Gviz uses the exact same chromosome naming conventions as for the UCSC-based IdeogramTrack data. You will have to provide a more concrete example of your problem.

Florian

ADD COMMENT • link 9.4 years ago florian.hahne@novartis.com ★ 1.6k