mutation-waterfall

Python library for visualizing mutation landscape as waterfall diagram.

Gallery

Mutational landscape of TCGA-LAML cohorts.

Usage

Input format

Input file should be formatted as below (tab-delimited):

Sample	Mutation
S1	Gene1
S1	Gene2
S1	Gene3
S2	Gene2
S2	Gene4
...
S100	Gene130
S100	Gene142

Plotting

Plotting mutation waterfall plot can be done with mutation_waterfall.plot.plot function. Specify the path to your input file as an mutation_list_file positional argument.

import mutation_waterfall.plot as mwp
mwp.plot(mutation_list_file='input.txt')

Executing command above results in a beautiful waterfall plot.

Tweaking parameters

You can specify the number of genes to be shown with n_genes parameter (default: 30).

mwp.plot('input_txt', n_genes=5)

You can specify the matplotlib axis of the waterfall plot with ax parameter.

import matplotlib.pyplot as plt
fig = plt.figure()
# Draw first waterfall in the left side.
ax = fig.add_subplot(121)
mwp.plot('input.txt', ax=ax)
# Draw second waterfall in the right side.
ax = fig.add_subplot(122)
mwp.plot('input2.txt', ax=ax)

plt.tight_layout()
plt.savefig('waterfall.png')

You can save waterfall plot to an image file by specifying file parameter.

mwp.plot('input_txt', file='waterfall.png')