def test_get_mutations():
res = context_client.get_mutations(['BRAF'], ['A375_SKIN'])
assert res is not None
assert res.get('A375_SKIN') is not None
assert res['A375_SKIN'].get('BRAF') is not None
assert res['A375_SKIN']['BRAF'] == ['V600E']
assert unicode_strs(res)
def test_get_mutations():
res = context_client.get_mutations('BRAF', 'A375_SKIN')
assert(res is not None)
assert(res.get('BRAF') is not None)
assert(res['BRAF'].get('A375_SKIN') is not None)
assert(res['BRAF']['A375_SKIN'] == 1.0)
assert unicode_strs(res)
def set_context(self, cell_type):
"""Set protein expression data and mutational status as node attribute
This method uses :py:mod:`indra.databases.context_client` to get
protein expression levels and mutational status for a given cell type
and set a node attribute for proteins accordingly.
Parameters
----------
cell_type : str
Cell type name for which expression levels are queried.
The cell type name follows the CCLE database conventions.
Example: LOXIMVI_SKIN, BT20_BREAST
"""
node_names = [node['n'] for node in self.cx['nodes']]
res_expr = context_client.get_protein_expression(
node_names, [cell_type])
res_mut = context_client.get_mutations(node_names, [cell_type])
res_expr = res_expr.get(cell_type)
res_mut = res_mut.get(cell_type)
if not res_expr:
msg = 'Could not get protein expression for %s cell type.' % \
cell_type
logger.warning(msg)
if not res_mut:
msg = 'Could not get mutational status for %s cell type.' % \
cell_type
logger.warning(msg)
if not res_expr and not res_mut:
return
self.cx['networkAttributes'].append({
'n': 'cellular_context',
'v': cell_type
})
counter = 0
for node in self.cx['nodes']:
amount = res_expr.get(node['n'])
mut = res_mut.get(node['n'])
if amount is not None:
node_attribute = {
'po': node['@id'],
'n': 'expression_amount',
'v': int(amount)
}
self.cx['nodeAttributes'].append(node_attribute)
if mut is not None:
is_mutated = 1 if mut else 0
node_attribute = {
'po': node['@id'],
'n': 'is_mutated',
'v': is_mutated
}
self.cx['nodeAttributes'].append(node_attribute)
if mut is not None or amount is not None:
counter += 1
logger.info('Set context for %d nodes.' % counter)
def set_CCLE_context(self, cell_types):
"""Set context of all nodes and node members from CCLE."""
self.get_gene_names()
# Get expression and mutations from context client
exp_values = \
context_client.get_protein_expression(self._gene_names, cell_types)
mut_values = \
context_client.get_mutations(self._gene_names, cell_types)
# Make a dict of presence/absence of mutations
muts = {cell_line: {} for cell_line in cell_types}
for cell_line, entries in mut_values.items():
if entries is not None:
for gene, mutations in entries.items():
if mutations:
muts[cell_line][gene] = 1
else:
muts[cell_line][gene] = 0
# Create bins for the exp values
# because colorbrewer only does 3-9 bins and I don't feel like
# reinventing color scheme theory, this will only bin 3-9 bins
def bin_exp(expression_dict):
d = expression_dict
exp_values = []
for line in d:
for gene in d[line]:
val = d[line][gene]
if val is not None:
exp_values.append(val)
thr_dict = {}
for n_bins in range(3, 10):
bin_thr = np.histogram(np.log10(exp_values), n_bins)[1][1:]
thr_dict[n_bins] = bin_thr
# this dict isn't yet binned, that happens in the loop
binned_dict = {x: deepcopy(expression_dict) for x in range(3, 10)}
for n_bins in binned_dict:
for line in binned_dict[n_bins]:
for gene in binned_dict[n_bins][line]:
# last bin is reserved for None
if binned_dict[n_bins][line][gene] is None:
binned_dict[n_bins][line][gene] = n_bins
else:
val = np.log10(binned_dict[n_bins][line][gene])
for thr_idx, thr in enumerate(thr_dict[n_bins]):
if val <= thr:
binned_dict[n_bins][line][gene] = thr_idx
break
return binned_dict
binned_exp = bin_exp(exp_values)
context = {'bin_expression': binned_exp, 'mutation': muts}
self._context['CCLE'] = context
def set_CCLE_context(self, cell_types):
"""Set context of all nodes and node members from CCLE."""
self.get_gene_names()
# Get expression and mutations from context client
exp_values = \
context_client.get_protein_expression(self._gene_names, cell_types)
mut_values = \
context_client.get_mutations(self._gene_names, cell_types)
# Make a dict of presence/absence of mutations
muts = {cell_line: {} for cell_line in cell_types}
for cell_line, entries in mut_values.items():
if entries is not None:
for gene, mutations in entries.items():
if mutations:
muts[cell_line][gene] = 1
else:
muts[cell_line][gene] = 0
# Create bins for the exp values
# because colorbrewer only does 3-9 bins and I don't feel like
# reinventing color scheme theory, this will only bin 3-9 bins
def bin_exp(expression_dict):
d = expression_dict
exp_values = []
for line in d:
for gene in d[line]:
val = d[line][gene]
if val is not None:
exp_values.append(val)
thr_dict = {}
for n_bins in range(3, 10):
bin_thr = np.histogram(np.log10(exp_values), n_bins)[1][1:]
thr_dict[n_bins] = bin_thr
# this dict isn't yet binned, that happens in the loop
binned_dict = {x: deepcopy(expression_dict) for x in range(3, 10)}
for n_bins in binned_dict:
for line in binned_dict[n_bins]:
for gene in binned_dict[n_bins][line]:
# last bin is reserved for None
if binned_dict[n_bins][line][gene] is None:
binned_dict[n_bins][line][gene] = n_bins
else:
val = np.log10(binned_dict[n_bins][line][gene])
for thr_idx, thr in enumerate(thr_dict[n_bins]):
if val <= thr:
binned_dict[n_bins][line][gene] = thr_idx
break
return binned_dict
binned_exp = bin_exp(exp_values)
context = {'bin_expression': binned_exp,
'mutation': muts}
self._context['CCLE'] = context
def set_context(self, cell_type):
"""Set protein expression data and mutational status as node attribute
This method uses :py:mod:`indra.databases.context_client` to get
protein expression levels and mutational status for a given cell type
and set a node attribute for proteins accordingly.
Parameters
----------
cell_type : str
Cell type name for which expression levels are queried.
The cell type name follows the CCLE database conventions.
Example: LOXIMVI_SKIN, BT20_BREAST
"""
node_names = [node['n'] for node in self.cx['nodes']]
res_expr = context_client.get_protein_expression(node_names,
[cell_type])
res_mut = context_client.get_mutations(node_names,
[cell_type])
res_expr = res_expr.get(cell_type)
res_mut = res_mut.get(cell_type)
if not res_expr:
msg = 'Could not get protein expression for %s cell type.' % \
cell_type
logger.warning(msg)
if not res_mut:
msg = 'Could not get mutational status for %s cell type.' % \
cell_type
logger.warning(msg)
if not res_expr and not res_mut:
return
self.cx['networkAttributes'].append({'n': 'cellular_context',
'v': cell_type})
counter = 0
for node in self.cx['nodes']:
amount = res_expr.get(node['n'])
mut = res_mut.get(node['n'])
if amount is not None:
node_attribute = {'po': node['@id'],
'n': 'expression_amount',
'v': int(amount)}
self.cx['nodeAttributes'].append(node_attribute)
if mut is not None:
is_mutated = 1 if mut else 0
node_attribute = {'po': node['@id'],
'n': 'is_mutated',
'v': is_mutated}
self.cx['nodeAttributes'].append(node_attribute)
if mut is not None or amount is not None:
counter += 1
logger.info('Set context for %d nodes.' % counter)
def get_mutations(self, gene, cell_line):
if cell_line in self.mut:
mut = self.mut[cell_line].get(gene, [])
return {cell_line: {gene: mut}}
else:
return context_client.get_mutations([gene], [cell_line])
def set_context(self, *args, **kwargs):
"""Set protein expression data as node attribute
This method uses :py:mod:`indra.databases.context_client` to get
protein expression levels for a given cell type and set a node
attribute for proteins accordingly.
Parameters
----------
cell_type : str
Cell type name for which expression levels are queried.
The cell type name follows the CCLE database conventions.
Example: LOXIMVI_SKIN, BT20_BREAST
bin_expression : bool
If True, the gene expression will be put into 5 bins based on
all gene expression values. An additional bin is used to indicate
that the context_client returned None.
user_bins : int
If specified, split the expression levels into the given number
of bins. If not specified, default will be 5.
"""
cell_type = kwargs.get('cell_type')
if not cell_type:
logger.warning('No cell type given.')
return
# Collect all gene names in network
gene_names = []
for node in self._nodes:
members = node['data'].get('members')
if members:
gene_names += list(members.keys())
else:
if node['data']['name'].startswith('Group'):
continue
gene_names.append(node['data']['name'])
# Get expression and mutation from context client
exp = context_client.get_protein_expression(gene_names, cell_type)
mut = context_client.get_mutations(gene_names, cell_type)
if not exp:
logger.warning('Could not get context for %s cell type.' %
cell_type)
return
else:
exp = {k: v[cell_type] for k, v in exp.items()}
if not mut:
logger.warning('Could not get mutations for %s cell type.' %
cell_type)
return
else:
mut = {k: v[cell_type] for k, v in mut.items()}
# Get expression and mutation for specific gene
def get_expr_mut(name, expr_data, mut_data):
amount = expr_data.get(name)
if amount is None:
expression = None
else:
expression = np.log10(amount)
mutation = mut_data.get(name)
if mutation is not None:
mutation = int(mutation)
else:
mutation = 0
return expression, mutation
# Set node properties for expression and mutation
for node in self._nodes:
members = node['data'].get('members')
if members:
for member in members.keys():
expression, mutation = get_expr_mut(member, exp, mut)
node['data']['members'][member]['expression'] = expression
node['data']['members'][member]['mutation'] = mutation
node['data']['expression'] = None
node['data']['mutation'] = 0
else:
if node['data']['name'].startswith('Group'):
node['data']['expression'] = None
node['data']['mutation'] = 0
else:
expression, mutation = get_expr_mut(
node['data']['name'], exp, mut)
node['data']['expression'] = expression
node['data']['mutation'] = mutation
# Binning for the purpose of assigning colors
if kwargs.get('bin_expression'):
# how many bins? If not specified, set to 5
n_bins = 5
user_bins = kwargs.get('n_bins')
if type(user_bins) == int:
n_bins = user_bins
if n_bins > 9:
n_bins = 9
logger.info('Only 9 bins allowed. Setting n_bins = 9.')
if n_bins < 3:
n_bins = 3
logger.info('Need at least 3 bin. Setting n_bins = 3.')
# Create color scale for unmutated gene expression
# feed in hex values from colorbrewer2 9-class PuBuGn
wt_hexes = [
'#f7fcf5', '#e5f5e0', '#c7e9c0', '#a1d99b', '#74c476',
'#41ab5d', '#238b45', '#006d2c', '#00441b'
]
exp_wt_colorscale = _build_color_scale(wt_hexes, n_bins)
# tack on a gray for no expression data
exp_wt_colorscale.append('#bdbdbd')
self._exp_colorscale = exp_wt_colorscale
# create color scale for mutated gene expression
# feed in hex values from colorbrewer2 9-class YlOrRd
mut_hexes = [
'#fff5eb', '#fee6ce', '#fdd0a2', '#fdae6b', '#fd8d3c',
'#f16913', '#d94801', '#a63603', '#7f2704'
]
exp_mut_colorscale = _build_color_scale(mut_hexes, n_bins)
# tack on a gray for no expression data
exp_mut_colorscale.append('#bdbdbd')
self._mut_colorscale = exp_mut_colorscale
# capture the expression levels of every gene in nodes
exp_lvls = [n['data'].get('expression') for n in self._nodes]
# capture the expression levels of every gene in family members
m_exp_lvls = []
for n in self._nodes:
if n['data'].get('members'):
members = n['data']['members']
for m in members:
m_exp_lvls.append(members[m]['expression'])
# combine node expressions and family expressions
exp_lvls = exp_lvls + m_exp_lvls
# get rid of None gene expressions
exp_lvls = [x for x in exp_lvls if x is not None]
# bin expression levels into n equally sized bins
# bin n+1 reserved for None
# this returns the bounds of each bin. so n_bins+1 bounds.
# get rid of first value which is the leftmost bound
bin_thr = np.histogram(exp_lvls, n_bins)[1][1:]
# iterate over nodes
for n in self._nodes:
# if node has members set member bin_expression values
if n['data'].get('members'):
members = n['data']['members']
for m in members:
# if expression is None, set to bin index n_bins
if members[m]['expression'] is None:
members[m]['bin_expression'] = n_bins
else:
for thr_idx, thr in enumerate(bin_thr):
if members[m]['expression'] <= thr:
members[m]['bin_expression'] = thr_idx
break
# set bin_expression for the node itself
if n['data']['expression'] is None:
n['data']['bin_expression'] = n_bins
else:
for thr_idx, thr in enumerate(bin_thr):
if n['data']['expression'] <= thr:
n['data']['bin_expression'] = thr_idx
break
def set_CCLE_context(self, cell_types):
"""Set context of all nodes and node members from CCLE."""
self.get_gene_names()
gene_names = self._gene_names
exp = {}
mut = {}
# context_client gives back a dict with genes as keys.
# prefer lines keys, so this will need to be transposed
def transpose_context(context_dict):
d = context_dict
d_genes = [x for x in d]
d_lines = [x for x in d[d_genes[0]]]
transposed = {x: {y: d[y][x] for y in d_genes} for x in d_lines}
return transposed
# access the context service in chunks of cell types.
# it will timeout if queried with larger chunks.
while len(cell_types) > 0:
cell_types_chunk = cell_types[:10]
del cell_types[:10]
exp_temp = context_client.get_protein_expression(gene_names,
cell_types_chunk)
exp_temp = transpose_context(exp_temp)
for e in exp_temp:
exp[e] = exp_temp[e]
mut_temp = context_client.get_mutations(gene_names,
cell_types_chunk)
mut_temp = transpose_context(mut_temp)
for m in mut_temp:
mut[m] = mut_temp[m]
# create bins for the exp values
# because colorbrewer only does 3-9 bins and I don't feel like
# reinventing color scheme theory, this will only bin 3-9 bins
def bin_exp(expression_dict):
d = expression_dict
exp_values = []
for line in d:
for gene in d[line]:
val = d[line][gene]
if val is not None:
exp_values.append(val)
thr_dict = {}
for n_bins in range(3, 10):
bin_thr = np.histogram(np.log10(exp_values), n_bins)[1][1:]
thr_dict[n_bins] = bin_thr
# this dict isn't yet binned, that happens in the loop
binned_dict = {x: deepcopy(expression_dict) for x in range(3, 10)}
for n_bins in binned_dict:
for line in binned_dict[n_bins]:
for gene in binned_dict[n_bins][line]:
# last bin is reserved for None
if binned_dict[n_bins][line][gene] is None:
binned_dict[n_bins][line][gene] = n_bins
else:
val = np.log10(binned_dict[n_bins][line][gene])
for thr_idx, thr in enumerate(thr_dict[n_bins]):
if val <= thr:
binned_dict[n_bins][line][gene] = thr_idx
break
return binned_dict
binned_exp = bin_exp(exp)
context = {'bin_expression': binned_exp,
'mutation': mut}
self._context['CCLE'] = context
def test_get_mutations_cell_type_missing():
mutations = context_client.get_mutations(['BRAF'], ['A375_SKIN', 'XYZ'])
assert 'A375_SKIN' in mutations
assert mutations['A375_SKIN']['BRAF'] == ['V600E']
assert 'XYZ' in mutations
assert not mutations['XYZ']['BRAF']
def get_mutations(self, gene, cell_line):
if cell_line in self.mut:
mut = self.mut[cell_line].get(gene, [])
return {cell_line: {gene: mut}}
else:
return context_client.get_mutations([gene], [cell_line])
def test_get_mutations_gene_missing():
mutations = context_client.get_mutations(['BRAF', 'XYZ'], ['A375_SKIN'])
assert ('A375_SKIN' in mutations)
assert (mutations['A375_SKIN']['BRAF'] == ['V600E'])
assert (not mutations['A375_SKIN']['XYZ'])
def set_context(self, *args, **kwargs):
"""Set protein expression data as node attribute
This method uses :py:mod:`indra.databases.context_client` to get
protein expression levels for a given cell type and set a node
attribute for proteins accordingly.
Parameters
----------
cell_type : str
Cell type name for which expression levels are queried.
The cell type name follows the CCLE database conventions.
Example: LOXIMVI_SKIN, BT20_BREAST
bin_expression : bool
If True, the gene expression will be put into 5 bins based on
all gene expression values. An additional bin is used to indicate
that the context_client returned None.
user_bins : int
If specified, split the expression levels into the given number
of bins. If not specified, default will be 5.
"""
cell_type = kwargs.get('cell_type')
if not cell_type:
logger.warning('No cell type given.')
return
# Collect all gene names in network
gene_names = []
for node in self._nodes:
members = node['data'].get('members')
if members:
gene_names += list(members.keys())
else:
if node['data']['name'].startswith('Group'):
continue
gene_names.append(node['data']['name'])
# Get expression and mutation from context client
exp = context_client.get_protein_expression(gene_names, cell_type)
mut = context_client.get_mutations(gene_names, cell_type)
if not exp:
logger.warning('Could not get context for %s cell type.' %
cell_type)
return
else:
exp = {k: v[cell_type] for k, v in exp.items()}
if not mut:
logger.warning('Could not get mutations for %s cell type.' %
cell_type)
return
else:
mut = {k: v[cell_type] for k, v in mut.items()}
# Get expression and mutation for specific gene
def get_expr_mut(name, expr_data, mut_data):
amount = expr_data.get(name)
if amount is None:
expression = None
else:
expression = np.log10(amount)
mutation = mut_data.get(name)
if mutation is not None:
mutation = int(mutation)
else:
mutation = 0
return expression, mutation
# Set node properties for expression and mutation
for node in self._nodes:
members = node['data'].get('members')
if members:
for member in members.keys():
expression, mutation = get_expr_mut(member, exp, mut)
node['data']['members'][member]['expression'] = expression
node['data']['members'][member]['mutation'] = mutation
node['data']['expression'] = None
node['data']['mutation'] = 0
else:
if node['data']['name'].startswith('Group'):
node['data']['expression'] = None
node['data']['mutation'] = 0
else:
expression, mutation = get_expr_mut(node['data']['name'],
exp, mut)
node['data']['expression'] = expression
node['data']['mutation'] = mutation
# Binning for the purpose of assigning colors
if kwargs.get('bin_expression'):
# how many bins? If not specified, set to 5
n_bins = 5
user_bins = kwargs.get('n_bins')
if type(user_bins) == int:
n_bins = user_bins
if n_bins > 9:
n_bins = 9
logger.info('Only 9 bins allowed. Setting n_bins = 9.')
if n_bins < 3:
n_bins = 3
logger.info('Need at least 3 bin. Setting n_bins = 3.')
# Create color scale for unmutated gene expression
# feed in hex values from colorbrewer2 9-class PuBuGn
wt_hexes = ['#f7fcf5', '#e5f5e0', '#c7e9c0', '#a1d99b', '#74c476',
'#41ab5d', '#238b45', '#006d2c', '#00441b']
exp_wt_colorscale = _build_color_scale(wt_hexes, n_bins)
# tack on a gray for no expression data
exp_wt_colorscale.append('#bdbdbd')
self._exp_colorscale = exp_wt_colorscale
# create color scale for mutated gene expression
# feed in hex values from colorbrewer2 9-class YlOrRd
mut_hexes = ['#fff5eb', '#fee6ce', '#fdd0a2', '#fdae6b', '#fd8d3c',
'#f16913', '#d94801', '#a63603', '#7f2704']
exp_mut_colorscale = _build_color_scale(mut_hexes, n_bins)
# tack on a gray for no expression data
exp_mut_colorscale.append('#bdbdbd')
self._mut_colorscale = exp_mut_colorscale
# capture the expression levels of every gene in nodes
exp_lvls = [n['data'].get('expression') for n in self._nodes]
# capture the expression levels of every gene in family members
m_exp_lvls = []
for n in self._nodes:
if n['data'].get('members'):
members = n['data']['members']
for m in members:
m_exp_lvls.append(members[m]['expression'])
# combine node expressions and family expressions
exp_lvls = exp_lvls + m_exp_lvls
# get rid of None gene expressions
exp_lvls = [x for x in exp_lvls if x is not None]
# bin expression levels into n equally sized bins
# bin n+1 reserved for None
# this returns the bounds of each bin. so n_bins+1 bounds.
# get rid of first value which is the leftmost bound
bin_thr = np.histogram(exp_lvls, n_bins)[1][1:]
# iterate over nodes
for n in self._nodes:
# if node has members set member bin_expression values
if n['data'].get('members'):
members = n['data']['members']
for m in members:
# if expression is None, set to bin index n_bins
if members[m]['expression'] is None:
members[m]['bin_expression'] = n_bins
else:
for thr_idx, thr in enumerate(bin_thr):
if members[m]['expression'] <= thr:
members[m]['bin_expression'] = thr_idx
break
# set bin_expression for the node itself
if n['data']['expression'] is None:
n['data']['bin_expression'] = n_bins
else:
for thr_idx, thr in enumerate(bin_thr):
if n['data']['expression'] <= thr:
n['data']['bin_expression'] = thr_idx
break