gviz library plot 2 gene loci in the same figure
2
0
Entering edit mode
tangming2005 ▴ 190
@tangming2005-6754
Last seen 5 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 • 1.6k views
ADD COMMENT •
0
Entering edit mode
@florianhahnenovartiscom-3784
Last seen 5.6 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 •
0
Entering edit mode

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 •
0
Entering edit mode
@florianhahnenovartiscom-3784
Last seen 5.6 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 •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 564 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6