Improving agarose gels to increase readability

[kcorreia]

• allowing sample ids to be shown on gel or longer names (maybe rotated for longer names)
• invert colours (I see that there is code commented out right now) which is better for printing
• having mass/weights applied to fragments that make some fragments bolder than others. For example, NEB ladder has most fragments with 30-60 ng, except 500bp, 1000bp, 3000bp with 120ng.

[BjornFJohansson]

The first point is a great suggestion. The code would need to make sensible choices as to the placement and text size. Any ideas about that? Perhaps some code I could reuse.

The second is easy:

im = gel([ GeneRuler_1kb_plus, [band, ]])
from PIL import ImageOps
ImageOps.invert(im)

This could be made into a method, but I thought it might be simpler as is.

The third should be there already. Look at the ladders.py module.

[kcorreia]

I'm not sure on how to implement text with PIL but soon enough I'll get frustrated with manually annotating printouts and learn more about PIL.

[BjornFJohansson]

Simply adding the size below the band is easy. The problem is what to do when the bands are in close proximity.
Have a look at BandWitch from Edinburgh https://github.com/Edinburgh-Genome-Foundry/BandWitch
It has a sort of gel simulator for schematic gels.

https://www.blog.pythonlibrary.org/2021/02/02/drawing-text-on-images-with-pillow-and-python