[Biopython] graphics library suggestions?

[Peter Cock]

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
>
>