I want to remove an edge attribute from a Graph object in python-igraph. The equivalent igraph R function is cleverly called delete_edge_attr. I haven't been able to find an equivalent function/method in Python... is there one?
If not, is there another way to do it? (I tried a simple g.es['edge_attr']= [] but this didn't work).
Example Code
g = ig.Graph.Tree(10, 2) #Generate random graph
g_betweenness = g.betweenness() #Calculate betweenness for graph
g['betweenness'] = betweenness #Assign betweenness as edge attribute
print(g.attributes())
g['betweenness'] = [] #Attempt to remove betweenness edge attribute (incorrect)
print(g.attributes())
Output
['betweenness']
['betweenness']
Desired output
['betweenness']
[]
You might not be able to set it to an empty array, but your intuition about directly altering the EdgeSequence was already pretty good. You can simply delete the argument with Python's internal del(), I've included a minimal example below:
import igraph
# minimal graph
G = igraph.Graph()
G.add_vertices(2)
G.add_edge(0,1)
# add your property
G.es['betweenness'] = [1]
# print edge attribute (note the difference to your example)
print(G.es.attribute_names())
# output: ['weight']
# delete argument
del(G.es['weight'])
# print again
print(G.es.attribute_names())
# output: []
I have this code:
def get_field(odb, step, frame, field, element):
if field == 'E':
function = get_strain
for f in odb.steps[step].frames[frame].fieldOutputs[field].getSubset(region=element_set).values:
data = function(f.data)
dict_data[index] = data
index += 1
return dict_data
I want to include section points and section category. What should I change in this code to achieve that?
You need to use another getSubset:
fo = ..... fieldOutput object
f = fo.getSubset(sectionPoint=sp)
Section point objects can be found in the odb:
odbname = 'mine.odb'
odb = session.odbs[odbname]
sp = odb.sectionCategories.values()[0]
If you want a particular section point number, each section Point object has the property
sp.number
I'm trying to create an array in python that will contain all the pairwise distances between every pair of nodes on a phylogenetic tree. I'm currently using dendropy to do this. (I initially looked at biopython but couldn't find an option to do this). The code I have so far looks like this:
import dendropy
tree_data = []
tree = dendropy.Tree.get(path="gonno_microreact_tree.nwk",schema="newick")
pdc = tree.phylogenetic_distance_matrix()
for i, t1 in enumerate(tree.taxon_namespace[:-1]):
for t2 in tree.taxon_namespace[i+1:]:
tip_pair = {}
tip_dist_list = []
tip_pair[t1] = t2
distance = pdc(t1, t2)
tip_dist_list.append(tip_pair)
tip_dist_list.append(distance)
tree_data.append(tip_dist_list)
print tree_data
This works well except for the way it writes the tip labels. For example an entry in the tree_data list looks like this:
[{<Taxon 0x7fc4c160b090 'ERS135651'>: <Taxon 0x7fc4c160b150 'ERS135335'>}, 0.0001294946558138355]
But the tips in the newick file are just labelled ERS135651 and ERS135335 respectively. How can I get dendropy to write the array with just the original tip labels so this entry would look like this:
[{ERS135651:ERS135335}, 0.0001294946558138355]
(Also I read the dendropy documentation and I'm aware that it says to use treecalc to do this, like this:
pdc = treecalc.PatristicDistanceMatrix(tree)
But I just get an error saying the command does not exist:
AttributeError: 'module' object has no attribute 'PairisticDistanceMatrix'
)
Any suggestions for how I can get this working?
Converting the tip labels to a string converted them to the name surrounded by speech marks, e.g.:
t1 = str(t1)
print t1
Gives:
"'ERS135651'"
So using string splicing to remove the extra speech marks works to convert the tip label back to it's proper name, e.g.:
t1 = t1.replace("'","")
I have a problem removing multiple edges in igraph using Python.
I have tried this, but it does not work:
for e in g.es:
if e.is_multiple() is True:
g.es.delete(e)
I even tried
for e in g.es:
if e.is_multiple() is True:
helptuple = e.tuple
source = helptuple[0]
target = helptuple[1]
eid = g.get_eid(source, target)
g.delete_edges(eid)
Is there another solution?
Try this:
def simplify(multiple=True, loops=True, combine_edges=None):
it is a function from the API.
multiple -> whether to remove multiple edges.
read more here:
https://igraph.org/python/doc/api/igraph._igraph.GraphBase.html#simplify
I have been working with pygraph on some project. I completed this example, it works fine.
Now, the problem is the following: the graph is drawn in a picture format (gif). What I need is to get the actual coordinates for each node for the graph layout shown on the gif image. How do I do this? I've been trying and trying, but couldn't find solution to this problem. I thought the the problem's solution would be somehow with manipulating one of the two following lines:
gv.layout(gvv,'dot')
gv.render(gvv,'png','europe.png')
Thanks in advance!
You can add the layout information into the graph with :
gv.render(gvv)
and then find out the position of a node getting its attribute pos :
n_france = gv.findnode(gvv, "France")
pos = gv.getv(n_france, "pos")
Then depending on what you want to do, you might need to convert dot coordinates into png image coordinates. You can get useful information from here :
http://www.graphviz.org/faq/#FaqCoordTransformation
It explains in great details the computation from the graph-units to image pixels.
Hope that this is what you are looking for.
I just found a similar solution that works perfectly for my needs
pos = nx.drawing.nx_agraph.graphviz_layout(G, prog='dot', args='-Grankdir=LR')
cheers!
Using pydotplus you can load in and parse a dot/gv file and interrogate the data structure pydotplus produces, but this internal representation seems not to initially possess all the node attributes, like pos, unless they were already in the file.
But you can also call .write_dot() to produce a much more verbose dot file version. If you parse this then the resulting data structure seems to have pos of all the nodes (and even pos for the splines)
Note: maybe best to index the nodes by name not by index because any text with square brackets after it in the verbose file will be parsed as a node, so the node list may have spurious extra elements.
In the following (slightly edited) experiment at the Spyder prompt I have a terse dot file interior.gv (that does not have pos for nodes) which I .graph_from_dot_file(), then .write_dot(). Then .graph_from_dot_file() again on the verbose generated file, and so find the pos as required.
import pydotplus as pdp
interior = pdp.graphviz.graph_from_dot_file('interior.gv')
interior.write_dot('interior2.dot')
Out[210]: True
interior2 = pdp.graphviz.graph_from_dot_file('interior2.dot')
interior2.get_nodes()[3].get_pos()
Out[214]: '"213.74,130"'
Networkx can do this:
import networkx as nx
def setup_europe():
G = nx.Graph()
G.add_edge("Portugal", "Spain")
G.add_edge("Spain","France")
G.add_edge("France","Belgium")
G.add_edge("France","Germany")
G.add_edge("France","Italy")
G.add_edge("Belgium","Netherlands")
G.add_edge("Germany","Belgium")
G.add_edge("Germany","Netherlands")
G.add_edge("England","Wales")
G.add_edge("England","Scotland")
G.add_edge("Scotland","Wales")
G.add_edge("Switzerland","Austria")
G.add_edge("Switzerland","Germany")
G.add_edge("Switzerland","France")
G.add_edge("Switzerland","Italy")
G.add_edge("Austria","Germany")
G.add_edge("Austria","Italy")
G.add_edge("Austria","Czech Republic")
G.add_edge("Austria","Slovakia")
G.add_edge("Austria","Hungary")
G.add_edge("Denmark","Germany")
G.add_edge("Poland","Czech Republic")
G.add_edge("Poland","Slovakia")
G.add_edge("Poland","Germany")
G.add_edge("Czech Republic","Slovakia")
G.add_edge("Czech Republic","Germany")
G.add_edge("Slovakia","Hungary")
return G
G = setup_europe()
Write a dot file:
nx.write_dot(G, '/tmp/out.dot')
Compute the position of the nodes:
pos = nx.pygraphviz_layout(G, prog = 'dot')
print(pos)
# {'Netherlands': (713.86, 167.0), 'Italy': (473.86, 389.0), 'Czech Republic': (100.86, 241.0), 'Portugal': (879.86, 315.0), 'England': (1024.9, 241.0), 'Denmark': (568.86, 167.0), 'Poland': (100.86, 167.0), 'Scotland': (1024.9, 389.0), 'France': (571.86, 315.0), 'Belgium': (713.86, 19.0), 'Austria': (320.86, 167.0), 'Slovakia': (156.86, 315.0), 'Wales': (990.86, 315.0), 'Switzerland': (473.86, 241.0), 'Hungary': (294.86, 241.0), 'Germany': (465.86, 93.0), 'Spain': (879.86, 241.0)}
Render an png:
agraph = nx.to_agraph(G)
agraph.draw("/tmp/europe.png", format = 'png', prog = 'dot')
Using just pydot/dot you can do it by generating the SVG and then reading the position of the nodes from the SVG. It is a bit hacky, but works reliably enough
from xml.dom import minidom
import pydot
from io import BytesIO
def extract_node_positions(
in_dot: pydot.Dot
) -> Dict[str, Tuple[str, float, float]]:
"""
Extract the x,y positions from a pydot graph by rendering
Args:
in_dot: the graph to render
Returns:
a list of all the nodes
Examples:
>>> g = pydot.Dot()
>>> g.add_node(pydot.Node("A"))
>>> g.add_node(pydot.Node("B"))
>>> g.add_node(pydot.Node("C"))
>>> g.add_edge(pydot.Edge("A", "B"))
>>> g.add_edge(pydot.Edge("B", "C"))
>>> extract_node_positions(g)
{'A': ('A', 27.0, -157.8), 'B': ('B', 27.0, -85.8), 'C': ('C', 27.0, -13.8)}
"""
node_mapping = {f'node{i}': k.get_name()
for i, k in enumerate(in_dot.get_nodes(), 1)}
svg_io = BytesIO(in_dot.create_svg())
doc = minidom.parse(svg_io) # parseString also exists
node_dict = {node_mapping[p.getAttribute('id')]: (c_text.firstChild.data,
float(c_text.getAttribute('x')),
float(c_text.getAttribute('y')))
for p in doc.getElementsByTagName("g") if "node" == p.getAttribute('class').lower()
for c_text in p.getElementsByTagName('text')
}
doc.unlink()
return node_dict
To directly access the results from the Graphviz rendering command (e.g. dot) as binary data string from within Python instead of writing to a file, use the pipe()-method of your Graph or Digraph object:
h = Graph('hello', format='svg')
h.edge('Hello', 'World')
print(h.pipe().decode('utf-8'))
I struggled with this recently, and the answers here were some help but not quite there. The suggestions about networkx are on the right track. Networkx uses pygraphviz to interface with graphviz, and so you can instead use pygraphviz directly if you wish:
import pygraphviz as pgv
G = pgv.AGraph(strict=False,directed=True)
# add nodes and edges
G.add_edge(1,2)
G.add_edge(2,1)
# generate a layout--this creates `pos` attributes for both nodes and edges
G.layout(prog="dot")
#change something about the graph that would change the layout, e.g.,
edge = G.get_edge("1", "2")
edge.attr["label"] = "test label"
# create the graph using the layout already generated; note, do not provide `prog`
G.draw("test.pdf")
# compare it to a newly generated layout
G.draw("test2.pdf", prog="dot")
The important part is to not provide prog to the draw command if you want to use the node and edge positions already generated by the layout command. I see now this is stated in the pygraphviz docstring for draw. BTW, it is does the same as prog="neato" with the -n2 argument. Looking at the sources, pygraphviz calls graphviz to generate the layout.