bioplotz: A package for plotting 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)

Chromosome Plot

import matplotlib.pyplot as plt
import bioplotz as bp

fig, ax, mapper = bp.chromosome(chr_len_db, chr_order, inner_data=bed_data, centro_db=centro_pos,
                                inner_value_type="numeric", orientation="vertical", **kwargs)
plt.colorbar(mapper, ax=ax, shrink=0.5)

# for drawing telomeres, we need a dict of telomeres
# the telomere dict is like below:
# chr_telo_db = {"Chr1": "start", "Chr2": "end", "Chr3": "both"}
# then add codes below
left_telo_list = []
right_telo_list = []
for _ in range(len(chr_order)):
    chrn = chr_order[_]
    if not chrn in chr_telo_db:
        continue
    if chr_telo_db[chrn] == "start":
        left_telo_list.append(_)
    elif chr_telo_db[chrn] == "end":
        right_telo_list.append(_)
    elif chr_telo_db[chrn] == "both":
        left_telo_list.append(_)
        right_telo_list.append(_)

# the value of color and s should be adjusted by user manually
plt.scatter([_ for _ in left_telo_list], [0 for _ in left_telo_list], color="blue", s=50)
plt.scatter([_ for _ in right_telo_list], [chr_len_db[chr_order[_]] for _ in right_telo_list], color="blue", s=50)

• If value_type is numeric, the return value mapper will be a mappable which could be used with plt.colorbar, else None

Gene Cluster Plot

import bioplotz as bp

fig, ax = bp.genecluster(gene_list)

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)

Details of color_kws
if color_mod is "match", the struct and default values of color_kws is like below:

# the default color of background colors is "white", 
# if there are not be set or set to None, 
# the default color of text colors is "black",
# if there are not be set or set to None
# user can overwrite any of them by set color_kws like:
# color_kws = {"match_color": "black", "match_background_color": "grey"} 
color_kws = {
    "match_color": 'blue',
    "match_background_color": None,
    "mismatch_color": 'red',
    "mismatch_background_color": None,
    "highlight_positions": None,
    "highlight_color": 'green',
    "highlight_background_color": None
}

if color_mod is "base", the struct and default values of color_kws is like below:

# the default color of text is "black" and default color of background is set below
# user can overwrite color of any charactor or add color for new charactor like *, -, ?
# by set color_kws like:
# color_kws = {"base_color": {"-": "white}, "base_background_color": {"-", "yellow"}}

color_kws = {
    "base_color": {},
    "base_background_color": {
        "A": "salmon", "a": "salmon",
        "T": "lightgreen", "t": "lightgreen",
        "G": "orange", "g": "orange",
        "C": "steelblue", "c": "steelblue",
        "U": "tomato", "u": "tomato",
        "F": "khaki", "f": "khaki",
        "D": "cadetblue", "d": "cadetblue",
        "N": "coral", "n": "coral",
        "E": "yellowgreen", "e": "yellowgreen",
        "Q": "plum", "q": "plum",
        "H": "orchid", "h": "orchid",
        "L": "darkseagreen", "l": "darkseagreen",
        "I": "yellow", "i": "yellow",
        "K": "lightseagreen", "k": "lightseagreen",
        "O": "darkkhaki", "o": "darkkhaki",
        "M": "palevioletred", "m": "palevioletred",
        "P": "sandybrown", "p": "sandybrown",
        "R": "palegreen", "r": "palegreen",
        "S": "peru", "s": "peru",
        "V": "violet", "v": "violet",
        "W": "mediumturquoise", "w": "mediumturquoise",
        "Y": "deepskyblue", "y": "deepskyblue"
    }
}

colors for base:

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, it would find the matplotlib defautl monospaced fonts, user can also set custom font like "Courier New", with the codes below.

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.monospace'] = 'Courier New'