def getNodeSizes(net,size_by="strength",minsize=2.0,maxsize=6.0):
"""Returns a dictionary {node:size} for visualizations. The sizes
are set using either node strength"""
nodeSizes={}
if size_by=="strength":
if hasattr(net,'matrixtype'):
if net.matrixtype==0:
net=transforms.dist_to_weights(net)
strengths = netext.strengths(net)
maxs = max(strengths.values())
mins = min(strengths.values())
if maxs==mins:
A=0
else:
A=(maxsize-minsize)/(maxs-mins)
B=maxsize-A*maxs
for node in net:
nodeSizes[node]=A*strengths[node]+B
elif size_by=="fixed":
for node in net:
nodeSizes[node]=maxsize
else:
numeric_props=netext.getNumericProperties(net)
if size_by in numeric_props:
values=[]
for node in net:
values.append(net.nodeProperty[size_by][node])
minval=min(values)
maxval=max(values)
if maxval==minval:
A=0
else:
A=(maxsize-minsize)/(maxval-minval)
B=maxsize-A*maxval
for node in net:
nodeSizes[node]=A*net.nodeProperty[size_by][node]+B
return nodeSizes
def getNodeSizes(net, size_by="strength", minsize=2.0, maxsize=6.0):
"""Returns a dictionary {node:size} for visualizations. The sizes
are set using either node strength"""
nodeSizes = {}
if size_by == "strength":
if hasattr(net, 'matrixtype'):
if net.matrixtype == 0:
net = transforms.dist_to_weights(net)
strengths = netext.strengths(net)
maxs = max(strengths.values())
mins = min(strengths.values())
if maxs == mins:
A = 0
else:
A = (maxsize - minsize) / (maxs - mins)
B = maxsize - A * maxs
for node in net:
nodeSizes[node] = A * strengths[node] + B
elif size_by == "fixed":
for node in net:
nodeSizes[node] = maxsize
else:
numeric_props = netext.getNumericProperties(net)
if size_by in numeric_props:
values = []
for node in net:
values.append(net.nodeProperty[size_by][node])
minval = min(values)
maxval = max(values)
if maxval == minval:
A = 0
else:
A = (maxsize - minsize) / (maxval - minval)
B = maxsize - A * maxval
for node in net:
nodeSizes[node] = A * net.nodeProperty[size_by][node] + B
return nodeSizes
def getNodeColors(net,colorwith="strength",useColorMap="orange",parentnet=[]):
"""Returns a dictionary {node:color}. The colors are set based
on either node strengh (colorwith="strength", default)
or any nodeProperty. For cases where e.g. nodes which have been thresholded
out (k=0), the input parameter parentnet can be used - parentnet should contain the original
network *before* thresholding, i.e. containing all original nodes and
their attributes. IF parentnet is given, i) if strength is used, its nodes
which are NOT in net colored gray, ii) if properties
are used, its nodes are colored similarly to those nodes in net. Also the
dictionary which is returned contains then all nodes in parentnet"""
myNodeColors=setColorMap(useColorMap)
nodeColors={}
if colorwith=="strength":
if hasattr(net,'matrixtype'):
if net.matrixtype==0:
net=transforms.dist_to_weights(net)
strengths = netext.strengths(net)
max_value = max(strengths.values())
min_value = min(strengths.values())
if len(parentnet)>0: # if we want the dict to include nodes not in net
for node in parentnet:
if node in net: # if the node is in net, use its strength for color
nodeColors[node]=setColor(strengths[node],(min_value,max_value),myNodeColors)
else: # otherwise color it gray
nodeColors[node]=(0.5,0.5,0.5)
else:
for node in net: # if parentnet not given, just color nodes by strength
nodeColors[node]=setColor(strengths[node],(min_value,max_value),myNodeColors)
else:
numeric_props=netext.getNumericProperties(net)
# first check if colorwith is a numeric property
if colorwith in numeric_props:
values=[]
if len(parentnet)>0: # again if we want to include nodes not in net
for node in parentnet: # first get min and max value of property
values.append(parentnet.nodeProperty[colorwith][node])
min_value=min(values)
max_value=max(values)
for node in parentnet: # then set colors according to property
nodeColors[node]=setColor(parentnet.nodeProperty[colorwith][node],(min_value,max_value),myNodeColors)
else: # otherwise do the above for nodes in net
for node in net:
values.append(net.nodeProperty[colorwith][node])
min_value=min(values)
max_value=max(values)
for node in net:
nodeColors[node]=setColor(net.nodeProperty[colorwith][node],(min_value,max_value),myNodeColors)
else:
# colorwith is not a numeric property, so look up unique values
# and give them integer numbers
values={} # empty dict for values
if len(parentnet)>0:# if there are nodes not in net
props=list(set(parentnet.nodeProperty[colorwith].values()))
else:
props=list(set(net.nodeProperty[colorwith].values()))
#Check if properties can be converted to colors:
if isListOfColors(props):
propToColor={}
cc=matplotlib.colors.ColorConverter()
for p in props:
propToColor[p]=cc.to_rgb(p)
if len(parentnet)>0:
for node in parentnet:
nodeColors[node]=propToColor[parentnet.nodeProperty[colorwith][node]]
else:
for node in net:
nodeColors[node]=propToColor[parentnet.nodeProperty[colorwith][node]]
else:
for i,prop in enumerate(props):
values[prop]=i+1
# now all property strings have a numerical value
min_value=1
max_value=max(values.values())
if len(parentnet)>0:
for node in parentnet:
nodeColors[node]=setColor(values[parentnet.nodeProperty[colorwith][node]],(min_value,max_value),myNodeColors)
else:
for node in net:
nodeColors[node]=setColor(values[net.nodeProperty[colorwith][node]],(min_value,max_value),myNodeColors)
if len(nodeColors)==0: # finally if for whatever reason no nodes were colored, just set them gray
if len(parentnet)>0:
for node in parentnet:
nodeColors[node]=(0.5,0.5,0.5)
else:
for node in net:
nodeColors[node]=(0.5, 0.5, 0.5)
return nodeColors
def getNodeColors(net,
colorwith="strength",
useColorMap="orange",
parentnet=[]):
"""Returns a dictionary {node:color}. The colors are set based
on either node strengh (colorwith="strength", default)
or any nodeProperty. For cases where e.g. nodes which have been thresholded
out (k=0), the input parameter parentnet can be used - parentnet should contain the original
network *before* thresholding, i.e. containing all original nodes and
their attributes. IF parentnet is given, i) if strength is used, its nodes
which are NOT in net colored gray, ii) if properties
are used, its nodes are colored similarly to those nodes in net. Also the
dictionary which is returned contains then all nodes in parentnet"""
myNodeColors = setColorMap(useColorMap)
nodeColors = {}
if colorwith == "strength":
if hasattr(net, 'matrixtype'):
if net.matrixtype == 0:
net = transforms.dist_to_weights(net)
strengths = netext.strengths(net)
max_value = max(strengths.values())
min_value = min(strengths.values())
if len(parentnet
) > 0: # if we want the dict to include nodes not in net
for node in parentnet:
if node in net: # if the node is in net, use its strength for color
nodeColors[node] = setColor(strengths[node],
(min_value, max_value),
myNodeColors)
else: # otherwise color it gray
nodeColors[node] = (0.5, 0.5, 0.5)
else:
for node in net: # if parentnet not given, just color nodes by strength
nodeColors[node] = setColor(strengths[node],
(min_value, max_value),
myNodeColors)
else:
numeric_props = netext.getNumericProperties(net)
# first check if colorwith is a numeric property
if colorwith in numeric_props:
values = []
if len(parentnet
) > 0: # again if we want to include nodes not in net
for node in parentnet: # first get min and max value of property
values.append(parentnet.nodeProperty[colorwith][node])
min_value = min(values)
max_value = max(values)
for node in parentnet: # then set colors according to property
nodeColors[node] = setColor(
parentnet.nodeProperty[colorwith][node],
(min_value, max_value), myNodeColors)
else: # otherwise do the above for nodes in net
for node in net:
values.append(net.nodeProperty[colorwith][node])
min_value = min(values)
max_value = max(values)
for node in net:
nodeColors[node] = setColor(
net.nodeProperty[colorwith][node],
(min_value, max_value), myNodeColors)
else:
# colorwith is not a numeric property, so look up unique values
# and give them integer numbers
values = {} # empty dict for values
if len(parentnet) > 0: # if there are nodes not in net
props = list(set(parentnet.nodeProperty[colorwith].values()))
else:
props = list(set(net.nodeProperty[colorwith].values()))
#Check if properties can be converted to colors:
if isListOfColors(props):
propToColor = {}
cc = matplotlib.colors.ColorConverter()
for p in props:
propToColor[p] = cc.to_rgb(p)
if len(parentnet) > 0:
for node in parentnet:
nodeColors[node] = propToColor[
parentnet.nodeProperty[colorwith][node]]
else:
for node in net:
nodeColors[node] = propToColor[
parentnet.nodeProperty[colorwith][node]]
else:
for i, prop in enumerate(props):
values[prop] = i + 1
# now all property strings have a numerical value
min_value = 1
max_value = max(values.values())
if len(parentnet) > 0:
for node in parentnet:
nodeColors[node] = setColor(
values[parentnet.nodeProperty[colorwith][node]],
(min_value, max_value), myNodeColors)
else:
for node in net:
nodeColors[node] = setColor(
values[net.nodeProperty[colorwith][node]],
(min_value, max_value), myNodeColors)
if len(
nodeColors
) == 0: # finally if for whatever reason no nodes were colored, just set them gray
if len(parentnet) > 0:
for node in parentnet:
nodeColors[node] = (0.5, 0.5, 0.5)
else:
for node in net:
nodeColors[node] = (0.5, 0.5, 0.5)
return nodeColors