[Biopython] graphics library suggestions?

[Peter Cock]

Yes :(

I remember trying another trick which was to set the PDF (or PNG)
image sizes depending on the length of the sequence (always same
height). However, the margin calculations were annoying...

Maybe you can see a nice improvement to the GenomeDiagram code
to make this kind of thing easier?

Peter

On Mon, May 4, 2015 at 3:11 PM, Katie Edmonds <betainverse at gmail.com> wrote:
> This is a pretty frustrating solution, since I would like all the figures I
> create now to be compatible with ones that I might make in the future. It
> seems like my only option is to make a generous guess about the maximum
> length I am likely to encounter in the future, and generate a dummy sequence
> of that size as a placeholder in every image I create now.
>
> On Mon, May 4, 2015 at 10:08 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>> Hi Katie,
>>
>> The scaling depends on the total length (bp) and tracks being shown.
>>
>> If you are trying to produce a set of figures with the same scale, scale
>> them all to the longest sequence - or draw it as a single multiple track
>> figure.
>>
>> e.g. This example (ignoring the cross links) has three sequences
>> of differing lengths:
>>
>> http://news.open-bio.org/news/2012/03/cross-links-in-genomediagram/
>>
>> Peter
>>
>> On Mon, May 4, 2015 at 2:42 PM, Katie Edmonds <betainverse at gmail.com>
>> wrote:
>> > It seems like even when I set the track height, the heights and the
>> > lengths
>> > of the arrows (per base pair) are always changing depending on the
>> > lengths
>> > of the sequences and the number of tracks in the figure. Is there any
>> > way
>> > that I am missing to nail down these proportions?
>> >
>> > On Thu, Apr 30, 2015 at 10:34 AM, Peter Cock <p.j.a.cock at googlemail.com>
>> > wrote:
>> >>
>> >> On Thu, Apr 30, 2015 at 3:15 PM, Katie Edmonds <betainverse at gmail.com>
>> >> wrote:
>> >> > Hi,
>> >> >
>> >> > I want to write a script that reads a list of genes from a table,
>> >> > including
>> >> > their start and endpoint on the chromosome, and generates vector
>> >> > graphics
>> >> > arrows on a line, with lengths and positions to scale for their size
>> >> > and
>> >> > location in the genome, colored by some value given in the table.
>> >> > Does
>> >> > anyone have any suggestions for a useful library for creating nice
>> >> > vector
>> >> > graphics arrows?
>> >> >
>> >> > Here's an example of what I'm talking about:
>> >> > https://github.com/betainverse/other/blob/master/gene_arrows.pdf
>> >> >
>> >> > Alternatively, is there already a good tool that does what I want?
>> >> >
>> >> > Thanks,
>> >> > Katie
>> >>
>> >> Biopython has GenomeDiagram (using ReportLab internally
>> >> to make PDF / SVG / PNG etc) which can do that. We have
>> >> various sigils (ways of drawing features), BIGARROW is
>> >> probably closest to the example you linked to.
>> >>
>> >> See: http://biopython.org/DIST/docs/tutorial/Tutorial.html
>> >>
>> >> Peter
>> >
>> >
>
>