Question: Create custom IdeogramTrack (Gviz)
1
gravatar for I-Hsuan Lin
3.6 years ago by
I-Hsuan Lin10
Taiwan
I-Hsuan Lin10 wrote:
Hello I want to ask if it is possible to create an IdeogramTrack object for a genome of my interest? If so, what information should I gather and also how can I create the object (what commands)? Regards, I-Hsuan
ideogram gviz • 1.3k views
ADD COMMENTlink modified 3.6 years ago by florian.hahne@novartis.com1.6k • written 3.6 years ago by I-Hsuan Lin10
Answer: Create custom IdeogramTrack (Gviz)
3
gravatar for florian.hahne@novartis.com
3.6 years ago by
Switzerland

Hi I-Hsuan,

there is some basic information on how to do that on the IdeogramTrack help page, im particular under the 'bands' argument section:

? IdeogramTrack

  bands: A ‘data.frame’ with the cytoband information for all

          available chromosomes on the genome similar to the data that

          would be fetched from UCSC. The table needs to contain the

          mandatory columns ‘chrom’, ‘chromStart’, ‘chromEnd’, ‘name’

          and ‘gieStain’ with the chromosome name, cytoband start and

          end coordinates, cytoband name and coloring information,

          respectively. This can be used when no connection to the

          internet is available or when the cytoband information has

          been cached locally to avoid the somewhat slow connection to

          UCSC.

So assuming that you have created the necessary IdeogramTrack data.frame, you could initialize the object like this

idTrack <- IdeogramTrack(genome="yourGenomeName", bands=yourBandsDataFrame)

Now where you get the bands information from is totally up to you. In the easiest case you would just use the chromosome lengths for the chromStart and chromEnd values, essentially creating Ideograms without banding.

Florian

 

ADD COMMENTlink written 3.6 years ago by florian.hahne@novartis.com1.6k

Thanks Florian!

Regarding the last comment, IdeogramTrack() will still requires the data.frame to contain the name and gieStain information. So what I did is give it arbitrary names and one of the valid stain values.

I-Hsuan

ADD REPLYlink written 3.6 years ago by I-Hsuan Lin10
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