[Bioperl-l] Re: patch xyplot.pm negative values Bio::Graphics/GMOD

Albert Vilella avilella at gmail.com
Mon Jun 13 05:56:27 EDT 2005

> I also have little experience on Bio::Graphics, but from my
> understanding I also think that draw_boxes and draw_scale needs to be
> modified. 
> I did this as well and you can see my experiments on
> http://genome.insilico.at/cgi-bin/gbrowse/nimblegen
> Though my approach is very hacky, I can share it. I made a copy to my
> private module gwxyplot.pm which is an overkill but good for
> experiments. I think this function should go into a new graph_type
> option in xyplot.
> I think my solution is similar to yours, If you want I can test your
> version on our gbrowse installation.

This morning (with more caffeine in my veins) I found out that my
previous patch was wrong: I confounded the middle-point with the
zero-point in the vertical axis...

> I still miss features to draw the scale:
> -) all over the detail view 
> -) also if no features are available, the empty scale should be drawn.
> -) do correct padding if scale is drawn.

Is this in only in GMOD side or does it also affect Bio::Graphics?

> In my approach I need to configure the min_score max_score otherwise the
> scale is not done correct which is not very good ...

So, basically, min_score, max_score and draw_scale parts need some work
so that gwxyplot changes can be merged to xyplot. Is that right?


> > PD: I haven't done anything about the log coordinates.

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