import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
import numpy as np
from transposonmapper.importing import load_default_files
from transposonmapper.processing import list_known_essentials
[docs]def profile_genome_plot(bar_width,l_genome,allinsertionsites_list,allcounts_binnedlist,summed_chr_length_dict,
middle_chr_position,chrom_list,variable,genes_currentchrom_pos_list,gene_pos_dict):
"""Plot function to show the whole insertion map throughout the genome
Parameters
----------
bar_width : int
The width for the histogram of the plot, by default None , which means internally the length of the genome over 1000
l_genome : int
The length of the genome in bp
allinsertionsites_list : list
List of insertions sites
allcounts_binnedlist : list
List of binned counts
summed_chr_length_dict : dict
The cumulative sum of the length of every chromosome
middle_chr_position : dict
Middle chromosome position per chromosome
chrom_list : list
A list of all the chromosomes
variable : str
It could be "transposons" or "reads"
genes_currentchrom_pos_list : list
List of genes per chromosome
gene_pos_dict : dict
Postion along the genome of every gene
"""
_,essential_file,_=load_default_files()
genes_essential_list=list_known_essentials(essential_file)
plt.figure(figsize=(19.0,9.0))
grid = plt.GridSpec(20, 1, wspace=0.0, hspace=0.0)
textsize = 12
textcolor = "#000000"
barcolor= "#333333"
chrom_color=(0.9,0.9,0.9,1.0)
essential_face_color="#00F28E"
non_essential_face_color="#F20064"
alpha=0.8
binsize = bar_width
ax = plt.subplot(grid[0:19,0])
ax.grid(False)
ax.tick_params(axis='x', which='major', pad=30)
axc = plt.subplot(grid[19,0])
axc.set_xlim(0,l_genome)
axc.tick_params(
axis='x', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
bottom=False, # ticks along the bottom edge are off
top=False, # ticks along the top edge are off
labelbottom=False) # labels along the bottom edge are off
axc.tick_params(
axis='y', # changes apply to the y-axis
which='both', # both major and minor ticks are affected
left=False, # ticks along the bottom edge are off
right=False, # ticks along the top edge are off
labelleft=False) # labels along the bottom edge are off
ax.set_xlim(0,l_genome)
# bar lines
ax.bar(allinsertionsites_list,allcounts_binnedlist,width=binsize,color=barcolor)
# chromosome lines
for chrom in summed_chr_length_dict:
ax.axvline(x = summed_chr_length_dict.get(chrom), linestyle='-', color=chrom_color)
ax.set_xticks(middle_chr_position)
ax.set_xticklabels(chrom_list, fontsize=textsize)
# Axis labels
if variable == "transposons":
ax.set_ylabel('Transposon Count', fontsize=textsize, color=textcolor)
elif variable == "reads":
ax.set_ylabel('Read Count', fontsize=textsize, color=textcolor)
# colored bars in the bottom
for gene in genes_currentchrom_pos_list:
if not gene_pos_dict.get(gene)[0] == 'Mito':
gene_start_pos = summed_chr_length_dict.get(gene_pos_dict.get(gene)[0]) + int(gene_pos_dict.get(gene)[1])
gene_end_pos = summed_chr_length_dict.get(gene_pos_dict.get(gene)[0]) + int(gene_pos_dict.get(gene)[2])
if gene in genes_essential_list:
axc.axvspan(gene_start_pos,gene_end_pos,facecolor=essential_face_color,alpha=alpha)
else:
axc.axvspan(gene_start_pos,gene_end_pos,facecolor=non_essential_face_color,alpha=alpha)
