Bubble plot, using scatter plot panels to visualize result from pathway analysis¶
One can include multiple panels, and customize size, colors of scatters.
In [1]:
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
# these use mummichog output pathway .tsv files
# more files can be used
INDIR = "../inputdata/"
input_files = ['mcg_pathwayanalysis_A.tsv', 'mcg_pathwayanalysis_B.tsv' ]
In [8]:
# read pathway analysis result from mummichog
def get_data(f):
'''
Input data: pathway overlap_size pathway_size p-value
'''
mydict = {}
w = open(f).read().splitlines()
# first 50 lines are usually enough; extra lines may exist in the pathway export table
for line in w[1: 50]:
a = line.split('\t')
mydict[a[0]] = -np.log10(float(a[3])) # a[4] if mummichog v1 result
return mydict
# read data
mydata = []
for ff in input_files: mydata.append( get_data(INDIR + ff) )
# manualy input pathway list.
#Edit below for different set/order of pathways
selected_pathways = '''Tryptophan metabolism
Glycosphingolipid metabolism
Methionine and cysteine metabolism
Ascorbate (Vitamin C) and Aldarate Metabolism
Glycerophospholipid metabolism
Galactose metabolism
Sialic acid metabolism
Alanine and Aspartate Metabolism
Carnitine shuttle
Purine metabolism'''
selected_pathways = [x.strip() for x in selected_pathways.splitlines()]
selected_pathways.reverse()
# plot
fig, myaxes = plt.subplots(figsize=(8, 6), nrows=1, ncols=2)
Y = range( len(selected_pathways) )
#
# plt.yticks(range(len(selected_pathways)), selected_pathways)
for ii in range(2):
X = [mydata[ii].get(path, 0) for path in selected_pathways]
print(X)
myaxes[ii].set_xlim( 1, 4.5 )
myaxes[ii].set_xticks(range(1, 5))
myaxes[ii].set_yticks(range(len(selected_pathways)))
myaxes[ii].set_yticklabels([]*len(selected_pathways))
#myaxes[ii].set_ylim( 0, 0.5+len(selected_pathways))
myaxes[ii].grid(True, color='w', linestyle='-', linewidth=2, alpha=0.3, zorder=0)
myaxes[ii].set_axis_bgcolor('0.9')
# change styles below. s stands for size of dots
myaxes[ii].scatter( X, Y, s=[30*x**2 for x in X], c='blue', linewidths =0, alpha=1, zorder=3)
myaxes[0].set_yticklabels(selected_pathways)
plt.tight_layout()
plt.show()
# comment out the last line and use this line to save file
# plt.savefig('good-bubbles-.pdf')
