I would like to automate the process of making an SVG representation of an individual ideogram, in the linear form seen (for example) at the top of a UCSC Genome Browser session. What data sources should I use to get the banding data?
I'd also be interested in any information about the format the data are presented in, so that I can translate it into a figure that includes band start/stop, centromere position, p/q arms, coordinate system data, etc.
•
written
by
Alex Reynolds
The ideogram is drawn from information stored in a "karyotype" track. ggbio can fetch this track automatically from UCSC, if it exists, and draw the ideogram.
plotIdeogram is the function to look at.
It looks like some source code might be here: http://bioconductor.org/packages/devel/bioc/html/ggbio.html
In the UCSC browser, the cytoBand are located in the cytoBand database:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.sql
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz
(...)
http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/cytoBand.sql (...)
or sometimes it's called 'cytoBandIdeo'
http://hgdownload.cse.ucsc.edu/goldenPath/canFam3/database/cytoBandIdeo.sql (...)
Log in to answer this question.
dup of
Drawing chromosome ideogams with data
Sorry, to be clearer: I'm not looking for third-party packages to draw them, but the actual sources of data that go into them, so that I can render a figure with my own code.