# -*- coding: utf-8 -*-
#
# This file is part of Sequana software
#
# Copyright (c) 2016 - Sequana Development Team
#
# File author(s):
# Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this software.
#
# website: https://github.com/sequana/sequana
# documentation: http://sequana.readthedocs.io
#
##############################################################################
from sequana.lazy import pandas as pd
from sequana.lazy import pylab
[docs]
class Boxplot(object):
"""Used to plot boxplot of fastq quality a la fastqc"""
def __init__(self, data):
# if data is a dataframe, keep it else, transform to dataframe
try:
self.df = pd.DataFrame(data)
except:
self.df = data
self.xmax = self.df.shape[1]
self.X = None
[docs]
def plot(self, color_line="r", bgcolor="grey", color="yellow", lw=4, hold=False, ax=None):
xmax = self.xmax + 1
if ax:
pylab.sca(ax)
if self.X is None:
X = range(1, self.xmax + 1)
pylab.fill_between(
X, self.df.mean() + self.df.std(), self.df.mean() - self.df.std(), color=color, interpolate=False
)
pylab.plot(X, self.df.mean(), color=color_line, lw=lw)
if self.df.mean().mean() < 40: # illumina
pylab.fill_between([0, xmax], [0, 0], [20, 20], color="red", alpha=0.3)
pylab.fill_between([0, xmax], [20, 20], [30, 30], color="orange", alpha=0.3)
pylab.fill_between([0, xmax], [30, 30], [41, 41], color="green", alpha=0.3)
pylab.ylim([0, 41])
else:
pylab.fill_between([0, xmax], [0, 0], [20, 20], color="red", alpha=0.3)
pylab.fill_between([0, xmax], [20, 20], [30, 30], color="orange", alpha=0.3)
pylab.fill_between([0, xmax], [30, 30], [101, 101], color="green", alpha=0.3)
pylab.ylim([0, 101])
pylab.xlim([0, self.xmax + 1])
pylab.title("Quality scores across all bases")
pylab.xlabel("Position in read (bp)")
pylab.ylabel("Quality")
pylab.grid(axis="x")
