[BioC] question regarding gviz

[Hahne, Florian]

Hi Elmar,
this is indeed a little tricky because the data in UCSC are spread across
several tables. I think you will indeed have to fetch it for each of these
tables individually. Looking at the table structure it seems that the data
are stored in a BED-like structure, and the color is encoded in the
itemRgb column. In your first attempt you didn't tell the UcscTrack
constructor how to map the columns in the downloaded tables to the
AnnotationTrack fields. You need to provide at least the mapping for the
start and end coordinates ('chromStart' and 'chromEnd' columns) in the
UCSC table, and to make use of the color information also the 'itemRgb'
column. The item names may also be useful, and we can get those from the
'name' column. Below is how a call would look like:

Broad1 <- UcscTrack(track='Broad ChromHMM',
table="wgEncodeBroadHmmGm12878HMM", trackType="AnnotationTrack",
genome='hg18', chromosome='chr18',
name='12878', from=44675486, to=44679944, start="chromStart",
end="chromEnd", feature="itemRgb", id="name", collapse=FALSE,
stacking="dense")

Note that I also turned off stacking for the track and collapsing, because
we want to force all items to be on one line. Now we just need to tell the
track how to color the items accordingly. That may look a bit exotic, in
the ind it is rather simple: I define a bunch of display parameters with
the same names as the features we downloaded from UCSC in the itemRgb
column. The values of these parameters are the colors that have been
stored as RGB values.

feat <- unique(feature(Broad1))
featCol <- setNames(as.list(rgb(t(sapply(strsplit(feat, ","),
as.numeric)), maxColorValue=255)), feat)
displayPars(Broad1) <- featCol

Now you would have to do the same for all your tables, so maybe sticking
the whole thing into lapply will make sense:


tracks <- lapply(c("wgEncodeBroadHmmGm12878HMM",
"wgEncodeBroadHmmH1hescHMM", "wgEncodeBroadHmmK562HMM",
"wgEncodeBroadHmmHepg2HMM", "wgEncodeBroadHmmHuvecHMM",
"wgEncodeBroadHmmHmecHMM"),
function(table){
	track <- UcscTrack(track='Broad ChromHMM', table=table,
trackType="AnnotationTrack", genome='hg18', chromosome='chr18',
		name=gsub("^wgEncodeBroadHmm|HMM$", "", table), from=44675486,
to=44679944, start="chromStart", end="chromEnd", feature="itemRgb",
id="name", collapse=FALSE, stacking="dense")

	feat <- unique(feature(track))
	featCol <- setNames(as.list(rgb(t(sapply(strsplit(feat, ","),
as.numeric)), maxColorValue=255)), feat)
	displayPars(track) <- featCol
	track
})

plotTracks(tracks)


Is that more or less what you were looking for?

Florian

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-- 






From:  "E.Tobi at lumc.nl" <E.Tobi at lumc.nl>
Date:  Friday, January 11, 2013 3:03 PM
To:  NIBR <florian.hahne at novartis.com>
Subject:  question regarding gviz


>Dear dr. Hahne,
> 
>We are using your package Gviz more and more in our department.
>
>I am currently trying to use the ³Broad ChromHMM² track
>(group=Regulation), which consists of 9 tables, in one panel using the
>original colors of the items.
>But I am having trouble recreating the following UCSC view:
> 
>
> 
> 
> 
> 
> 
> 
> 
>                  
>                  
>                  
>
>Somehow I am unable to 1. get it downloaded through the basic UcscTrack()
>function (currently going via rtracklayer as a run around) 2. collapse
>the different
> tracks in one similarly styled track as above.
> 
>Could you perhaps give me a pointer in the right direction to get this
>interesting feature in my pictures?
> 
>Broad1 <- UcscTrack(track='Broad ChromHMM',table =
>"wgEncodeBroadHmmGm12878HMM", trackType="AnnotationTrack", genome='hg18',
>chromosome='chr18',
>name='12878', from=44675486, to=44679944)
>Broad2 <- UcscTrack(track='Broad ChromHMM',table =
>"wgEncodeBroadHmmH1hescHMM", trackType="AnnotationTrack", genome='hg18',
>chromosome='chr18',
>name='hESC', from=44675486, to=44679944)
>Broad3 <- UcscTrack(track='Broad ChromHMM',table =
>"wgEncodeBroadHmmK562HMM", trackType="AnnotationTrack", genome='hg18',
>chromosome='chr18',
>name='K562', from=44675486, to=44679944)
>Broad4 <- UcscTrack(track='Broad ChromHMM',table =
>"wgEncodeBroadHmmHepg2HMM", trackType="AnnotationTrack", genome='hg18',
>chromosome='chr18',
>name='Hepg2', from=44675486, to=44679944)
>Broad5 <- UcscTrack(track='Broad ChromHMM',table =
>"wgEncodeBroadHmmHuvecHMM", trackType="AnnotationTrack", genome='hg18',
>chromosome='chr18',
>name='Huvec', from=44675486, to=44679944)
>Broad6 <- UcscTrack(track='Broad ChromHMM',table =
>"wgEncodeBroadHmmHmecHMM", trackType="AnnotationTrack", genome='hg18',
>chromosome='chr18',
>name='Hmec', from=44675486, to=44679944)
> 
> 
>Many thanks for any help or suggestion,
> 
>Best wishes
>Elmar Tobi
> 
> 
> 
> 
> 
> 
>