[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 #10 from Daniel.Nicorici at gmail.com  2009-12-07 13:56 EST -------


(In reply to comment #7)
> (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.)
>

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?

BR,
Daniel

> Cheers,
> 
> L.
> 


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