def test_recombinations_have_these_required_fields(self):
# deletions should be optional here
data = {
'nucleotide': 'TGTGCTCCCGAAGCGATGGGCGGATCTGAAAAGCTGGTCTTT',
'v_gene_name': 'TRBV25-1',
'v_ties': 'TRBV25-1,TRBV28',
'd_gene_name': 'TRBD2',
'd_ties': None,
'j_gene_name': 'TRBJ1-1',
'j_ties': None,
'v_deletion': None,
'd5_deletion': None,
'd3_deletion': None,
'j_deletion': None,
'vd_insertion': 0,
'dj_insertion': 27,
'v_end': 4,
'd_start': 5,
'd_end': 9,
'j_start': 37,
'sequence_status': 'Productive',
'cdr3_length': 42,
}
r = Recombination()
for key, value in data.items():
setattr(r, key, value)
r.save()
r_in_db = Recombination.objects.get()
for key, value in data.items():
self.assertEqual(
value, getattr(r_in_db, key), 'key value %s not equal' % key)
def vj_freq(self):
'''
Returns a list of lists containing frequences of each
v_family-j_gene pair and the clonofilter id
'''
clonofilters = sorted(self.clonofilters_all())
vj_counts_dict_dict= dict([(clonofilter.id, clonofilter.vj_counts_dict())
for clonofilter in clonofilters])
v_list = sorted(Recombination.v_gene_names())
j_list = sorted(Recombination.j_gene_names())
data = []
# Counts for the scatter plot
for clonofilter_id, vj_counts_dict in vj_counts_dict_dict.iteritems():
for v_index, v_family in enumerate(v_list):
for j_index, j_gene in enumerate(j_list):
data_point = []
data_point.append(v_list[v_index])
data_point.append(j_list[j_index])
if vj_counts_dict[v_family][j_gene]:
data_point.append(vj_counts_dict[v_family][j_gene])
else:
data_point.append(0)
# Append sample id
data_point.append(clonofilter_id);
if data_point[2] > 0:
data.append(data_point)
return data
def d3_test(request, comparison_id):
'''
This is a test of the d3 library.
'''
from clonotypes.models import Recombination
from django.utils import simplejson as json
from matplotlib.colors import rgb2hex
comparison = Comparison.objects.get(id=comparison_id)
clonofilters = sorted(comparison.clonofilters_all())
sample_names = dict([(clonofilter.id,str(clonofilter.sample)) for clonofilter in clonofilters])
vj_counts_dict_dict= dict([(clonofilter.id, clonofilter.vj_counts_dict())
for clonofilter in clonofilters])
clonofilter_colors = comparison.colors()
v_list = sorted(Recombination.v_family_names())
j_list = sorted(Recombination.j_gene_names())
data = []
# Counts for the scatter plot
for clonofilter_id, vj_counts_dict in vj_counts_dict_dict.iteritems():
for v_index, v_family in enumerate(v_list):
for j_index, j_gene in enumerate(j_list):
data_point = []
data_point.append(v_list[v_index])
data_point.append(j_list[j_index])
if vj_counts_dict[v_family][j_gene]:
data_point.append(vj_counts_dict[v_family][j_gene])
else:
data_point.append(0)
# Append sample id
data_point.append(clonofilter_id);
if data_point[2] > 0:
data.append(data_point)
# Functionality stats
comp_functionality = []
for cf in clonofilters:
cf_functionality = {}
values = {}
for key, value in cf.functionality_dict().iteritems():
values[key] = value
cf_functionality['key'] = cf.id
cf_functionality['values'] = values
comp_functionality.append(cf_functionality)
context = {'data': json.dumps(data),
'v_list': json.dumps(v_list),
'j_list': json.dumps(j_list),
'sample_names': json.dumps(sample_names),
'sample_colors': json.dumps(clonofilter_colors),
'comparison_id': comparison_id,
'functionality': json.dumps(comp_functionality),
}
return render(request, 'd3_test.html', context)
def vj_freq_ajax(request, comparison_id):
comparison = Comparison.objects.get(id=comparison_id)
sample_names = comparison.sample_names()
data = {'vjFreq': comparison.vj_freq(),
'vList': sorted(Recombination.v_gene_names()),
'jList': sorted(Recombination.j_gene_names()),
'sampleNames': sample_names,
}
return HttpResponse(json.dumps(data), mimetype='application/json')
def scatter_nav_tag(comparison):
from clonotypes.models import Recombination
import json
clonofilters = sorted(comparison.clonofilters_all())
vj_counts_dict_dict= dict([(clonofilter.id, clonofilter.vj_counts_dict())
for clonofilter in clonofilters])
v_list = sorted(Recombination.v_gene_names())
j_list = sorted(Recombination.j_gene_names())
data = []
# Counts for the scatter plot
for clonofilter_id, vj_counts_dict in vj_counts_dict_dict.iteritems():
for v_index, v_family in enumerate(v_list):
for j_index, j_gene in enumerate(j_list):
data_point = []
data_point.append(v_list[v_index])
data_point.append(j_list[j_index])
if vj_counts_dict[v_family][j_gene]:
data_point.append(vj_counts_dict[v_family][j_gene])
else:
data_point.append(0)
# Append sample id
data_point.append(clonofilter_id);
if data_point[2] > 0:
data.append(data_point)
# Functionality stats
comp_functionality = []
for cf in clonofilters:
cf_functionality = {}
values = {}
for key, value in cf.functionality_dict().iteritems():
values[key] = value
cf_functionality['key'] = cf.id
cf_functionality['values'] = values
comp_functionality.append(cf_functionality)
context = {'data': json.dumps(data),
'v_list': json.dumps(v_list),
'j_list': json.dumps(j_list),
'sample_names': json.dumps(comparison.sample_names()),
'sample_colors': json.dumps(comparison.colors()),
'comparison_id': comparison.id,
'functionality': json.dumps(comp_functionality),
}
return context
def j_usage_graph(request, clonofilter_id):
'''
Returns a PNG of j usage as a line graph
'''
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
import matplotlib.pyplot as plt
response = HttpResponse(content_type='image/png')
fig, ax = plt.subplots()
canvas = FigureCanvas(fig)
# variables which will contain data to be plotted
usage = []
gene_index = []
# Retreive the clonofilter
cf = ClonoFilter.objects.get(id=clonofilter_id)
# Get v usage data
j_usage_dict = cf.j_usage_dict()
# Get a list of v family names
j_gene_names = sorted(Recombination.j_gene_names())
# Convert v usage dict into two lists for plotting
for j_index, j_gene in enumerate(j_gene_names):
if j_gene in j_usage_dict:
usage.append(j_usage_dict[j_gene])
else:
usage.append(0)
gene_index.append(j_index)
# Generate the image
ax.plot(gene_index, usage, '-', marker='o')
# Axes labels and title
ax.set_title('%s J Usage' % cf.sample)
ax.set_xlabel('J Gene Family')
ax.set_ylabel('Usage')
xtickNames = plt.setp(ax, xticklabels=j_gene_names)
plt.setp(xtickNames, rotation=90, fontsize=9)
ax.xaxis.set_ticks(range(len(j_gene_names)))
canvas.print_png(response)
return response
def test_j_gene_names_returns_list_of_distinct_j_gene_names(self):
make_fake_patient_with_3_clonotypes()
self.assertIsInstance(Recombination.j_gene_names(), list)
self.assertEqual(
[u'TRBJ1-1', u'TRBJ2-4'], Recombination.j_gene_names())
def test_functionality_states_returns_list_of_all_functionality_states_in_db(self):
make_fake_patient_with_3_clonotypes()
self.assertIsInstance(Recombination.functionality_states(), list)
self.assertEqual([u'Productive', u'Out of frame'],
Recombination.functionality_states())
def test_vj_counts_returns_an_empty_2d_list_with_dimensions_len_vfam_by_jgene(self):
v_family_names = Recombination.v_gene_names()
j_gene_names = Recombination.j_gene_names()
vj_counts = self.f.vj_counts()
self.assertEqual(len(v_family_names), len(vj_counts))
self.assertEqual(len(j_gene_names), len(vj_counts[0]))
def bubble(request, clonofilter):
''' Takes in a filter and returns a bubble image generated by matplolib '''
# from matplotlib.figure import Figure
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
import matplotlib.pyplot as plt
import numpy as np
from math import sqrt
from mpl_toolkits.axes_grid1 import make_axes_locatable
import pylab
# Initialize required stuff for plotting
response = HttpResponse(content_type='image/png')
# fig = Figure()
# ax = fig.add_subplot(111)
fig, ax = plt.subplots()
canvas = FigureCanvas(fig)
# Initialize empty data variables
x = []
y = []
color = []
data = []
area = []
vj_counts_dict = clonofilter.vj_counts_dict()
# Calculate the plotting area by finding the number of v's and j's
v_list = sorted(Recombination.v_gene_names())
j_list = sorted(Recombination.j_gene_names())
width = len(v_list)
height = len(j_list)
for v_index, v_family in enumerate(v_list):
for j_index, j_gene in enumerate(j_list):
x.append(v_index)
y.append(j_index)
if vj_counts_dict[v_family][j_gene]:
color.append(vj_counts_dict[v_family][j_gene])
data.append(vj_counts_dict[v_family][j_gene])
else:
color.append(0)
data.append(0)
# Normalize bubble areas
if data:
# Scales the area of a v-j junction by the size of the plot
# and the maximum data value
area_norm_factor = (2.0 / max(data)) * width * height
area = [datapoint * area_norm_factor for datapoint in data]
# Use big outlines
# sct = ax.scatter(x, y, c=color, s=area, linewidths=2, edgecolor='w')
# Use small
sct = ax.scatter(
x, y, c=color, s=area, linewidths=1, edgecolor='lightgrey', alpha=.5)
# sct.set_alpha(0.5)
# Labels, legends, titles etc
# Set titles
ax.set_title('%s V-J Usage Bubbleplot' % clonofilter.sample)
ax.set_xlabel('V Gene Family')
ax.set_ylabel('J Gene')
# Add a grid
ax.yaxis.grid(True, linestyle='-', which='both', color='lightgrey',
alpha=0.5)
ax.xaxis.grid(True, linestyle='-', which='both', color='lightgrey',
alpha=0.5)
# Set the axes and plotting area
ax.set_xlim(-1, width)
ax.set_ylim(-1, height)
xtickNames = plt.setp(ax, xticklabels=v_list)
plt.setp(xtickNames, rotation=90, fontsize=9)
ax.xaxis.set_ticks(range(len(v_list)))
ytickNames = plt.setp(ax, yticklabels=j_list)
plt.setp(ytickNames, fontsize=9)
ax.yaxis.set_ticks(range(len(j_list)))
# Shrink the plot to make room for legends
box = ax.get_position()
ax.set_position([box.x0, box.y0, box.width * 0.8, box.height])
# Draw the bubble size legend
max_data = max(data)
bubbles = []
bubble_labels = []
# Exponentially decreasing areas from max_data to max_data * 2^-8
for bubble_area in [max_data * 1.35 ** (-exp) for exp in range(0, 15)]:
# Determine marker size
marker_size = sqrt(
bubble_area / max_data * (len(j_list) * len(v_list * 2)))
# Determine marker color. np.nextafter() is used because pylab.cm.jet
# function is looking for a range from [0,1)
marker_color = pylab.cm.jet(np.nextafter(bubble_area / max_data, -1))
bubbles.append(plt.Line2D(range(1), range(1), marker='o', markersize=marker_size, color=marker_color, linewidth=0, markeredgecolor="lightgrey", alpha=0.5))
bubble_labels.append('%g' % bubble_area)
# Draw the legend
#ax.legend(bubbles, bubble_labels, numpoints=1, loc='center left', bbox_to_anchor=(1.175, .5), prop={'size': 10})
ax.legend(bubbles, bubble_labels, numpoints=1, loc='center left', bbox_to_anchor=(1.175, .5), labelspacing=1.5, prop={'size': 10}, title="Counts")
# Colorbar
# Make the colorbar a bit smaller
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="2%", pad=0.05)
cb = plt.colorbar(sct, cax=cax)
# Old way
# cb = plt.colorbar(sct, ax=ax)
cb.set_label("Counts")
# Print the png and return
canvas.print_png(response)
return response
def bubble(request, comparison_id):
'''
Takes in a comparison id and generates a bubble plot such that
each clonofilter within the comparison instance gets its own color
'''
from matplotlib.figure import Figure
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
import matplotlib.pyplot as plt
from clonotypes.models import Recombination
from math import sqrt
import pylab
import numpy as np
comparison = Comparison.objects.get(id=comparison_id)
clonofilters = sorted(comparison.clonofilters_all())
response = HttpResponse(content_type='image/png')
fig = Figure()
canvas = FigureCanvas(fig)
ax = fig.add_subplot(111)
clonofilter_colors = comparison.colors_list()
x = []
y = []
color = []
data = []
area = []
# Calculate the plotting area by finding the number of v's and j's
v_list = sorted(Recombination.v_gene_names())
j_list = sorted(Recombination.j_gene_names())
width = len(v_list)
height = len(j_list)
# get a list of vj_counts
vj_counts_dict_list = [clonofilter.vj_counts_dict()
for clonofilter in clonofilters]
for clonofilter_index, vj_counts_dict in enumerate(vj_counts_dict_list):
for v_index, v_family in enumerate(v_list):
for j_index, j_gene in enumerate(j_list):
x.append(v_index)
y.append(j_index)
color.append(clonofilter_colors[clonofilter_index])
if vj_counts_dict[v_family][j_gene]:
data.append(vj_counts_dict[v_family][j_gene])
else:
data.append(0)
# Normalize area by the median and plot area
#area_norm_factor = (1.0/median(data)) * width * height
if data:
area_norm_factor = (2.0/max(data)) * width * height
area = [datapoint * area_norm_factor for datapoint in data]
sct = ax.scatter(x, y, c=color, s=area, linewidths=2, edgecolor='w')
sct.set_alpha(0.4)
# Labels, legends, titles etc
# Set titles
ax.set_title('V-J Usage Comparison')
ax.set_xlabel('V Gene Family')
ax.set_ylabel('J Gene')
# Add a grid
ax.yaxis.grid(True, linestyle='-', which='both', color='lightgrey',
alpha=0.5)
ax.xaxis.grid(True, linestyle='-', which='both', color='lightgrey',
alpha=0.5)
# Set the axes and plotting area
ax.set_xlim(-1, width)
ax.set_ylim(-1, height)
xtickNames = plt.setp(ax, xticklabels=v_list)
plt.setp(xtickNames, rotation=90, fontsize=9)
ax.xaxis.set_ticks(range(len(v_list)))
ytickNames = plt.setp(ax, yticklabels=j_list)
plt.setp(ytickNames, fontsize=9)
ax.yaxis.set_ticks(range(len(j_list)))
# Shrink the plot to make room for legends
box = ax.get_position()
ax.set_position([box.x0, box.y0, box.width * 0.8, box.height])
# Draw the bubble size legend
max_data = max(data)
bubbles = []
bubble_labels = []
# Labels for exponentially decreasing bubble sizes
for bubble_area in [max_data * 1.45 ** (-exp) for exp in range(0, 10)]:
# Determine marker size
marker_size = sqrt(
bubble_area / max_data * (len(j_list) * len(v_list * 2)))
marker_color = 'lightgrey'
bubbles.append(plt.Line2D(range(1), range(1), marker='o', markersize=marker_size, color=marker_color, linewidth=0, markeredgecolor="lightgrey", alpha=0.5))
bubble_labels.append('%g' % bubble_area)
# Labels for sample colors
for index, clonofilter in enumerate(clonofilters):
marker_size = sqrt(width * height/ 1.5)
marker_color = clonofilter_colors[index]
bubbles.append(plt.Line2D(range(1), range(1), marker='o', markersize=marker_size, color=marker_color, linewidth=0, markeredgecolor="lightgrey", alpha=0.5))
bubble_labels.append('%s' % clonofilter.sample)
ax.legend(bubbles, bubble_labels, numpoints=1, loc='center left', bbox_to_anchor=(1., .5), labelspacing=1.5, prop={'size': 10}, title="Counts")
canvas.print_png(response)
return response