[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 #7 from lpritc at scri.sari.ac.uk  2009-12-07 08:03 EST -------
(In reply to comment #6)
> 
> (In reply to comment #5)
> > Leighton and I had (some time ago now) chatted about a related enhancement
> > allowing the user to give the y-limits.
> 
> I think that it is need enhancement. Let's see if others think that same! ;-)

Oh, it definitely does! ;)  Thank you for taking the time to improve it.

> > With than in mind, it makes sense to
> > give the x-axis vertical position in terms of a y-coordinate (rather than a few
> > limited options like top, middle and bottom). This would be more flexible.
> 
> This sounds good and I agree that it is more flexible.

This is my preferred option.

> Indeed that options like "top, middle, bottom" are limited but still the
> scaling is done automatically and the user does not have to know in what range
> are his/her values are and what are the minimum and maximum and what axis
> position matches all the graphs which he/she wants to generate.
> 
> I am sure that this can be done better than I did it.

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)         # middle
x_axis_pos = median(data)   # top

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.)

Cheers,

L.


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