sc-zhang/bioplotz

A plot package for bioinformatics

Introduction

This is a package for plotting some images for bioinformatics.

Dependencies

Python modules:
    numpy
    matplotlib
    pandas

Installation

Install via pip

pip install bioplotz

Install from source code

pip install git+https://github.com/sc-zhang/bioplotz.git --user

Usage

Manhattan Plot

import bioplotz as bp

fig, ax = bp.manhattan(data, threshold=0, color=['orange', 'green'], threshold_line_color='blue', log_base=0,
                       reverse=False, xtick_labels=True, ytick_labels=True, ax=None, marker='.', s=1, **kwargs)

parameter	value type	explain
data	dict list	dict key: block name     value: [[x1,x2,...,xn], [y1,y2,...,yn]] list is a list like: [[x1,y1], [x2, y2], ..., [xn, yn]]
threshold	value list	value if only one threshold line to plot, Notice: if log_base was set, threshold values should be calculated with same log_base manunally, if reverse is True, threshold values should be set to its opposite number list if more than one threshold line need to plot, a list can be used for different lines, like: [threshold_value1, threshol_value2]
color	list	color is a list used for blocks, if the count of block greater than color count, it will be used circularly
threshold_line_color	value list	value if threshold is a single value list if threshold is a list
threshold_line_width	value	value the line width of threshold lines
block_line_width	value	value if there are only one color, the block line will display as border, the width is set by this parameter
log_base	value	log_base = 0 means not calucate value with log log_base != 0 means log base for log values with it
reverse	Boolean	if all data lower than 0, you may use it to show opposite values
other parameters	value	same with parameters used in pyplot.scatter

Chromosome Plot

import bioplotz as bp

fig, ax, clb = bp.chromosome(chr_len_db, chr_order, bed_data, centro_pos, value_type="numeric", orientation="vertical", **kwargs)

parameter	value type	Optional	Default	explain
chr_len_db	dict	No	-	key: chromosome name value: chromosome length
chr_order	list	Yes	None	list: the custom chromosome order, like: ["Chr1", "Chr3", "Chr2"] must same with keys in chr_len
bed_data	list	Yes	None	list: two dimension list, like: [[chrome name, start pos, end pos, value/color]]
centro_pos	dict	Yes	None	key: chromosome name value: middle position of centromere
value_type	str	Yes	numeric	numeric: the 4th column of bed_data should be value color: the 4th column of bed_data is color marker: different with other two types, it need 5 columns, the 4th column of bed_data is marker, the 5th column is color (marker is same with the parameter which be used in pyplot.scatter)
orientation	str	Yes	vertical	"vertical" or "horizontal"
cmap	str	Yes	gist_rainbow	cmap for colorbar
cmap_parts	int	Yes	100	how many parts for splitting cmap
s	float or array-like, shape(n,)	Yes	None	same with parameter s use in pyplot.scatter
other parameters	value	Yes	None	same with parameters used in pyplot.plot

• If value_type is numeric, the return value clb will be colorbar, else None

Gene Cluster Plot

import bioplotz as bp

fig, ax = bp.genecluster(gene_list)

parameter	value type	Optional	Default	explain
gene_list	list	No	-	list: 2-dimension list, like [[gene name, start pos, end pos, direct(+/-), color], ..., [gene name, start pos, end pos, direct(+/-), color]]
edgecolor	list str	Yes	None	list: same length with gene_list, like: ["green", "blue", ..., "red"] str: common edge color for all genes
edgewidth	int	Yes	1	edge width for all genes
lw	int	Yes	3	line width to show the genome backbone

Notice, the best figsize should be (gene count, 1), for example: plt.figure(figsize=(16, 1)), and the bbox_inches parameter which in savefig should be 'tight'.

Multi Alignment Plot

import bioplotz as bp

fig, ax = bp.multialign(data)

parameter	value type	Optional	Default	explain
data	dict	No	-	key: gene name value: alignment sequence
match_color	str	Yes	blue	color of matched bases
match_background_color	str	Yes	None	background color of matched bases
mismatch_color	str	Yes	red	color of mismatched bases
mismatch_background_color	str	Yes	None	background color of mismatched bases
base_per_line	int	Yes	80	base count to display for each line
highlight_positions	list	Yes	None	positions for highlighting, 0-base
highlight_color	str	Yes	green	color of highlighting positions in highlight_positions
highlight_background_color	str	Yes	None	background color of highlighting positions in highlight_positions
**kwargs	any	Yes	-	same with which use in ax.text

Notice, the figsize should be (base_per_line/10, x) where x=align_length/base_per_line*gene_count/5, and the font must be monospaced, like "Courier New", that sometimes user need add codes as following.

import matplotlib as mpl
import bioplotz as bp

basefont = mpl.font_manager.FontProperties(fname="/path/to/font.ttf")
fig, ax = bp.multialign(data, fontproperties=basefont)

or

plt.rcParams['font.sans-serif'] = 'Courier New'