karyopyploter

Table of Contents

• karyopyploter
  • Acknowledgements
  • Installation
  • Example usage
  • TODOs
  • License
  • Cytoband data

Acknowledgements

This project was based on the work by @Adoni5 and his repository pyryotype. It was made to provide similar functionality to what is being offered by KaryoploteR package, but in a more pythonic style, using Matplotlib as the basis, and giving the user full liberty to plot anything they want.

Installation

console pip install karyopyploter

Example usage

```python from karyopyploter import ( GENOME, plotideogram, makeideogramgrid, makegenomegrid, annotateideogram, addideogramcoordinates, reset_coordinates, zoom, ) from matplotlib import pyplot as plt from itertools import chain from pathlib import Path

OUTDIR = Path(file).parent.parent / "exampleoutputs" / "readmeexample" OUTDIR.mkdir(parents=True, existok=True) genome = GENOME.CHM13 fig, axes = plt.subplots( ncols=1, nrows=22, figsize=(11, 11), facecolor="white", ) for ax, contigname in zip(axes, [f"chr{i}" for i in chain(range(1, 23), "XY")]): chromosome = contigname plotideogram(ax, target=chromosome, genome=genome, label=contig_name)

similar to:

fig = plt.figure(figsize=(11, 11), facecolor="white") fig, , ideogramaxes = makeideogramgrid( target=[f"chr{contigname}" for contigname in chain(range(1, 23), "XY")], numsubplots=0, genome=genome, fig=fig, ) fig.savefig(TESTDIR / "ideogram_grid1.png", dpi=300) Will output: ![Example ideogram grid 1](https://raw.githubusercontent.com/vaslem/karyopyploter/main/example_outputs/readme_example/ideogram_grid1.png?raw=true) python

and with a subplots grid

fig, ax, ideogramaxes = makeideogramgrid( subplotwidth=15, gridparams=dict(hspace=1), ideogramfactor=0.3, target=[f"chr{contigname}" for contigname in chain(range(1, 5))], numsubplots=1, genome=genome, ) fig.savefig(TESTDIR / "ideogram_grid2.png", dpi=300) Will output: ![Example ideogram grid 2](https://raw.githubusercontent.com/vaslem/karyopyploter/main/example_outputs/readme_example/ideogram_grid2.png?raw=true) python

and with some regions annotated

regions = {'chr1':[(1000000,2000000, "red")], 'chr2':[(3000000, 4000000, 'blue')], 'chr3':[(5000000,6000000, (0,1,0)), (7000000,8000000, (1,0,0))]} for chr in regions: annotateideogram(ideogramaxes[chr], regions=regions[chr], genome=genome) fig.savefig(TESTDIR / "ideogramgrid3.png", dpi=300) Will output: ![Example ideogram grid 3](https://raw.githubusercontent.com/vaslem/karyopyploter/main/example_outputs/readme_example/ideogram_grid3.png?raw=true) python

maybe we want to zoom in on specific regions

zoomregions = {'chr1': (500000, 2500000), 'chr4': (3000000, 4000000)} for chr in zoomregions: zoom(ideogramaxes[chr], start=zoomregions[chr][0], stop=zoomregions[chr][1]) fig.savefig(OUTDIR / "ideogram_grid4.png", dpi=300) Will output: ![Example ideogram grid 4](https://raw.githubusercontent.com/vaslem/karyopyploter/main/example_outputs/readme_example/ideogram_grid4.png?raw=true)

or we want to show coordinates

for chr in zoomregions: addideogramcoordinates(ideogramaxes[chr]) resetcoordinates(ax[chr], ideogramaxes[chr]) fig.savefig(TESTDIR / "ideogramgrid5.png", dpi=300) ``` Will output:

TODOs

• Investigate the creation of circos plots, by polar transformation.
• Provide more detailed documentation, as some features are not described

License

karyopyploter is distributed under the terms of the BSD-3-Clause license. Feel free to use in both academic and commercial applications, and please consider to cite the software in your work.

Cytoband data

• HG38
• HG19
• CHM13