[Biopython-dev] [Bug 2964] placing x-axis of graph track at the bottom or top of the track in GenomeDiagram

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2964





------- Comment #13 from biopython-bugzilla at maubp.freeserve.co.uk  2010-05-19 11:11 EST -------
I've been looking at this myself recently (I'm drawing transcriptome read
coverage data which means I have no negative values), and tried a few things.

(In reply to comment #7 and #8)
> 
> By allowing the position of the axis to take any value within the data range,
> this still allows 'top', 'middle' and 'bottom' to be defined as functions of
> the data with, e.g.
> 
> x_axis_pos = min(data)          # bottom
> x_axis_pos = max(data)         # top
> x_axis_pos = median(data)   # middle
> 
> and also allows for explicit placing of the axis at specified points on the
> y-axis, or as other points that depend on the data (e.g. mean, quartiles,
> etc.)

There is a problem with this - the x-axis and other bits like the scale are
drawn by the Track object. This can contain multiple datasets, which can all
be using their own coordinate systems. In specifying the x-axis position we
can't therefore talk about max(data), min(data) or median(data) for the track
as a whole. What we can do is talk about bottom/middle/top (or even a float
between 0 and 1 to be more precise). This is quite easy but doesn't address
the plotting side of things...


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