Question

How to set track attributes in rtracklayer

0

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foehn ▴ 100

@foehn-16281

Last seen 3.2 years ago

United States

Hello,

I'm trying to use rtracklayer to view my data in UCSC genome browser, but have no idea how to set track attributes such as color or description. Manually setting up color and description in UCSC browser is rather tedious, so I would best avoid it but do it in the program.

Here is an example.

> library(rtracklayer)
> gr1 <- GRanges("chr1", IRanges(100001, 102000))
> gr2 <- gr1 + 3000

> session <- browserSession("UCSC")

> track(session, name = "gr1") <- gr1
> track(session, name = "gr2") <- gr2

> browserView(session, track = c("gr1", "gr2")) # This works but no track color or description set in the script

When I tried to set arguments color and description in track, the tracks were not uploaded at all.

> library(rtracklayer)
> gr1 <- GRanges("chr1", IRanges(100001, 102000))
> gr2 <- gr1 + 3000

> session <- browserSession("UCSC")

> track(session, name = "gr1", color = col2rgb("red")[, 1], description = "gr1") <- gr1
> track(session, name = "gr2", color = col2rgb("green")[, 1], description = "gr2") <- gr2

> browserView(session, track = c("gr1", "gr2"))
Error in resolveTrackIndex(object, value) : Unknown track(s): gr1, gr2

> "gr1" %in% trackNames(session)
[1] FALSE
> "gr2" %in% trackNames(session)
[1] FALSE

Probably I didn't use the package the correct way. Anyway, does anybody know how to do it? Thanks,

rtracklayer browserView browserSession • 1.3k views

ADD COMMENT • link updated 5.7 years ago by Michael Lawrence ★ 11k • written 5.7 years ago by foehn ▴ 100

score 2 · Accepted Answer · 2019-03-01

2

Entering edit mode

Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.9 years ago

United States

Thanks, this should be fixed in rtracklayer 1.42.2. It should also try to report an error when an upload fails. But that's just a heuristic.

ADD COMMENT • link 5.7 years ago Michael Lawrence ★ 11k

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Indeed, my current rtracklayer is version 1.42.1. I will try 1.42.2, thanks.

ADD REPLY • link 5.7 years ago foehn ▴ 100

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Note that 1.42.2 will become available after a couple of days.

ADD REPLY • link 5.7 years ago Michael Lawrence ★ 11k

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Entering edit mode

This is the result from the latest version. It appears something is still wrong.... Any idea? Thanks again.

> gr1 <- GRanges("chr1", IRanges(100001, 102000))
> gr2 <- gr1 + 3000
> session <- browserSession("UCSC")
> track(session, name = "gr1", color = col2rgb("red")[, 1], description = "gr1") <- gr1
Warning message:
In readChar(f, 1) :
  text connection used with readChar(), results may be incorrect
> track(session, name = "gr2", color = col2rgb("green")[, 1], description = "gr2") <- gr2
Warning message:
In readChar(f, 1) :
  text connection used with readChar(), results may be incorrect
> browserView(session, track = c("gr1", "gr2"))
Error in resolveTrackIndex(object, value) : Unknown track(s): gr1, gr2

> packageVersion("rtracklayer")
[1] ‘1.43.2’

ADD REPLY • link 5.7 years ago foehn ▴ 100

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The version is 1.42.2, not 1.43.2. If you're using devel, then you'll need 1.43.3.

ADD REPLY • link 5.7 years ago Michael Lawrence ★ 11k

0

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Very clear, thanks! Also, it seems bit tricky of bioconductor's versioning, as I would think 1.43.2 should naturally contain the bug fix from 1.42.2...