bismarkplot 1.0.1

A small library to plot Bismark methylation_exctractor reports.

BismarkPlot

A small library to plot Bismark methylation_extractor reports.

See the docs: https://shitohana.github.io/BismarkPlot

Right now only coverage2cytosine input is supported, but support for bismark2bedGraph will be added soon.

Installation

pip install bismarkplot

Example

First we need to initialize genome and BismarkFiles. genome is .gff or .bed file with gene coordinates. BismarkFiles is a class, which calculates data for all plots, so their types need to be specified when it is initialized.

import bismarkplot

file = 'path/to/genome.gff'

genome = bismarkplot.read_genome(
    file,
    flank_length=2000,
    min_length=4000
)

files = ['path/to/genomeWide1.txt', 'path/to/genomeWide2.txt']
bismark = bismarkplot.BismarkFiles(
    files, genome,
    flank_windows=500,
    gene_windows=2000,
    line_plot=True,
    heat_map=True,
    box_plot=True,
    bar_plot=True
)

Let's now draw plots themselves.

For line plots use (or draw_line_plots_all for all contexts)

bismark.draw_line_plots_filtered(
    context='CG',
    strand='+',
    smooth=.05,
    labels = ['exp1', 'exp2'],
    title = 'Plot for CG+'
) 

For heat maps use (or draw_heat_maps_all for all contexts)

bismark.draw_heat_maps_filtered(
    context='CG',
    strand='+',
    resolution=100,
    labels = ['exp1', 'exp2'],
    title = 'Heatmap for CG+'
)   

For box plot or bar plot use

bismark.draw_box_plot(strand_specific=True, labels=['exp1', 'exp2'])
bismark.draw_bar_plot(labels=['exp1', 'exp2'])