[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 #11 from lpritc at scri.sari.ac.uk  2009-12-08 03:49 EST -------
(In reply to comment #10)

> It looks a little bit confusing too me now because I see that there are two
> sides of the problem (or two bugs?), as following:
> 1) drawing a line orthogonal on y-axis at any position which represents the
> x-axis (this does not affect how the values are plotted and in what interval)
> 2) in the case of bar plotting (partially affects also linear plotting), the
> values should be drawn automatically from zero (zero on y-axis, i.e. x=0 and
> y=-inf...+inf) unless the user specify something else and not to be drawn by
> default from some arbitrary point, e.g. median, mean, etc., as it is done now. 
> 
> I have the feeling that the solution presented here affects only the point 1)
> and not 2).
> 
> Please, could you elaborate more such that maybe I could implement your
> suggestion?

I see why you've distinguished between the two cases, but I think they can be
handled by the earlier suggestion to implement the location of the x-axis in
the context of also allowing the user to set y-axis limits (see comment #5). 
It's the combination of allowing y-axis limits and the location of x-axis
crossing that gives the greatest flexibility.  For example, if y-limit
selection and x-axis crossing point were under user control...

...if you wanted to continue with the current behaviour, you'd not set any
y-limits, and not specify the location of the x-axis.

...if you wanted to draw short read coverage, you'd set the lower y-limit to 0,
and set the location of the x-axis to zero (if that was not the default).  This
should draw bars with their bases on the bottom/inner of the track, and the
scale running along the bottom/inner of the track. 

...if you wanted to represent some data as a bar graph, with a special meaning
for the mean (or median) value, you could optionally set y-limits, but have the
x-axis cross at mean(data) or median(data).  This should draw bars with their
bases on the x-axis, and the axis located at the mean/median value for the
data.

Does this help clarify what I meant, above?

L.


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