I want to make a graph with random node positions but it seems that the "pos" attribute for nodes does nothing. Here is a minimal example:
import graphviz
import pylab
from graphviz import Digraph
g = Digraph('G', filename='ex.gv',format='pdf')
g.attr(size='7')
g.node('1',pos='1,2')
g.node('2',pos='2,3')
g.node('3',pos='0,0')
g.edge('1','2')
g.edge('1','3')
graphviz.Source(g)
Any ideas of how achieve that?
Thanks in advance.
Although not 100% clear in the docs, I think pos is not supported in the dot engine on input. The fdp or neato engines do support pos on input for setting the initial position, and if you end the coordinate specification with '!', the coordinates will not change and thus become the final node position.
Play with a live example at https://beta.observablehq.com/#magjac/placing-graphviz-nodes-in-fixed-positions
This standalone python script generates a pdf with the expected node positions:
#!/usr/bin/python
import graphviz
from graphviz import Digraph
g = Digraph('G', engine="neato", filename='ex.gv',format='pdf')
g.attr(size='7')
g.node('1',pos='1,2!')
g.node('2',pos='2,3!')
g.node('3',pos='0,0!')
g.edge('1','2')
g.edge('1','3')
g.render()
Since SO does not support pdf uploading, here's a png image generated with the same code except format='png':
Without the exclamation marks you get:
Without any pos attributes at all you get a similar (but not exactly the same) result:
Related
I am using a combination of networkx, pygraphviz and graphviz to create and visualise graphs in python,
However I keep encountering utf-8 encoding errors when writing my dot file from my networkx graph that has greek letters as nodes.
I would like to be able to create dot graphs with nodes such as these: Κύριος, Θεός, Πᾶσα, Μέγας, Νέμεσις but am unable to do so.
Are there any encoding tricks I need to know about?
The example you posted works fine for me (using ipython with python 3.7) when using the correct dot file path.
import networkx as nx
from networkx.drawing.nx_pydot import write_dot
import graphviz as grv
n = "Νέμεσις"
G = nx.Graph()
G.add_node(n)
write_dot(G, 'test.dot')
grv.render('neato', 'svg', 'test.dot')
I'm using networkx (v2.5) for a dependency-analysis problem, and visualizing the data via graphviz / pygraphviz (v1.7) on ubuntu 20.04. The contents of each node (label field) is a code block - so I'd like it LEFT justified. The problem is I can't seem to change the default (CENTER justified).
X/Y: - my specific need is to make a png from a networkx graph where the node text is left-justified - I believe Graphviz/pygraphviz is the best ~trivial way to do so - but any FOSS way to accomplish this would be fine.
I successfully generate a png as desired, via the following simplified code, but the text is all center-justified.
from networkx import DiGraph, nx_agraph
from networkx.drawing.nx_agraph import write_dot
# graph is created via networkx:
graph = DiGraph()
graph.add_edge("node1", "node2")
graph.nodes["node1"]["label"] = get_code_sniped("node1")
# ...
# and converted / output to dot & png via (internally) pygraphviz
write_dot(graph, "/tmp/foo.dot") # appears correctly output
a_graph = nx_agraph.to_agraph(graph)
a_graph.layout(prog="dot")
# attempt to add attrs per defs in
# https://www.graphviz.org/doc/info/attrs.html#d:labeljust
a_graph.graph_attr.update(labeljust="l") # <----- has no effect on output
a_graph.graph_attr.update(nojustify=True) # <-/
a_graph.draw("/tmp/foo.png") # <-- PNG outputs successfully,
# but all node text is CENTER justified
How can I modify the node text (specifically left-justifying it) in the PNG generated from my networkx graph?
it appears there is (undocumented, AFAICT) upstream/native graphviz behavior w.r.t. inheriting graph-level attributes.
setting a_graph.graph_attr.update(... is insufficient, as it is not inherited by child elements. In order to for instance set fontname, the following works:
for node in formattable_graph.iternodes():
node.attr["fontname"] = "Liberation Mono"
also, for text-justification, one can control this on a Per line basis by changing the line ending "\l" (Note: that is two bytes in python as it's not an actual escape char) and "\r" for left and right (respectively).
this will LEFT justify all lines
graph.nodes["node1"]["label"] = """my
node label
with newlines
""".replace("\n", "\l")
I'm currently trying to build a block model using the python package networkx. I found that the function networkx.quotient_graph can be used for this job:
g_block = nx.quotient_graph(G=g, partition=node_list, relabel=True)
In the next step, I want to export the generated block graph "g_block" to a file to import it afterwards in a visualization tool that supports for example graphml-files.
nx.write_graphml(g_block, 'test_block.graphml')
However, this leads to the error:
{KeyError}class 'networkx.classes.graphviews.SubDiGraph'
Can someone help?
Currently networkx (version 2.2) doesn't support nested graphs in a way you can easily export and visualize. Consider using graphviz for handling your nested graph and export it to a dot format.
For working with a networkx version of the graph, you can transform the pygraphviz to a networkx graph and vise versa by keeping a 'graph' property for nodes (which is semantically a subgraph), similarly to the result of quotient_graph.
Here is an example of transforming a small networkx graph to pygraphviz with subgraphs, and exporting it as a dot file:
import networkx as nx
import pygraphviz as pgv
G = nx.erdos_renyi_graph(6, 0.5, directed=False)
node_list = [set([0, 1, 2, 3]), set([4, 5])]
pgv_G = pgv.AGraph(directed=True)
pgv_G.add_edges_from(G.edges())
for i, sub_graph in enumerate(node_list):
pgv_G.add_subgraph(sub_graph, name=str(i))
print(pgv_G)
pgv_G.write("test_pgv.dot")
Note that netwrokx also allows writing and reading 'dot' format (see example), however since there is no built-in support for nested graphs it's not too helpful for this purpose.
The reason you can't write the quotient_graph is twofold:
In a quotient_graph each node has a 'graph' property, which is a SubDiGraph (or a SubGraph, if the original graph is undirected). A SubDiGraph is a ReadOnlyGraph which means it is not possible to write it using the standard networkx.readwrite utils.
Even if we convert the SubDiGraph to a DiGraph, not every graph file format allows to encode a 'graph' property. For example, graphml format supports primitive properties such as booleans, integers etc. Read more here.
One solution that works is to solve the first issue by overriding the 'graph' property with a DiGraph copy of the original SubDiGraph. The second issue can be simply solved by using another file format (e.g., pickle format can work). Read about all supported formats here.
Following is a working example:
g_block = nx.quotient_graph(G=G, partition=node_list, relabel=True)
def subdigraph_to_digraph(subdigraph):
G = nx.DiGraph()
G.add_nodes_from(subdigraph.nodes())
G.add_edges_from(subdigraph.edges())
return G
for node in g_block:
g_block.nodes[node]['graph'] = subdigraph_to_digraph(g_block.nodes[node]['graph'])
nx.write_gpickle(g_block, "test_block.pickle")
This allows to write and load the nested graph for using with netwrokx, however for the purpose of using the exported file in a visualization tool this is not too helpful.
My task is to generate a graph from a dot file (using pydot) and then convert the same as networkx graph. The problem that I faced was that the attributes of Graph (as I have given in the .dot file) is not present in the networkx graph.
I also used read_dot() function which is again an error. My code is successfully working to visualize graphs but not its attribs.
My code is:
import pydot
import networkx as nx
(graph,) = pydot.graph_from_dot_file('1.dot')
G = nx.nx_pydot.from_pydot(graph)
nx.get_node_attributes(G,'1')
My output is {}
Pls help me to fix the problem
Thanks from Mathan :)
I am using networkX to draw a network plot from a distance matrix(emoji_sim, a DataFrame). Here is the code:
G = nx.from_numpy_matrix(np.array(emoji_sim))
nx.draw(G, edge_color='silver', node_color='lightsalmon', with_labels=True)
plt.show()
I know there is a way to relabel the nodes as:
G = nx.relabel_nodes(G, dict(zip(range(len(G.nodes())), range(1, len(G.nodes())+1))))
But I want to substitute the nodes label with images(possibly read from files or using Python Emoji package). Is there any way to do that? Thanks a lot!
To clarify, I am trying to substitute the actual circle with images.
The idea behind it is not very difficult but in order to get it to be displayed (at least on ubunto) it gave me some hard time as not all fonts support emoji. I shall display the straight forward way then some links that helped me in the end (maybe you will not need those).
From emoji cheat sheet from the emoji python package I picked up three to be shown as an example and here is the code.
G = nx.Graph()
G.add_nodes_from([0,1,2])
n0 = emoji.emojize(':thumbsup:',use_aliases=True)
n1 = emoji.emojize(':sob:',use_aliases=True)
n2 = emoji.emojize(':joy:',use_aliases=True)
labels ={0:n0,1:n1,2:n2}
nx.draw_networkx(G,labels=labels, node_color = 'w', linewidths=0, with_labels=True, font_family = 'Symbola' ,font_size = 35)
plt.show()
Difficulties encountered:
1- My machine is on ubunto 14.04, I could not display any emoji they always appeared as rectangles
Installed needed font Symbola using the following command (mentioned here):
sudo apt-get install ttf-ancient-fonts
2- Maplotlib (which networkx calls to draw) is not using the installed font.
From several useful discussions 1 2 3 4 5 6 I copied and pasted the .tff font file of Symbola in the default matplotib directory (where it fetches for fonts to use).
cp /usr/share/fonts/truetype/ttf-ancient-scripts/Symbola605.ttf /usr/share/matplotlib/mpl-data/fonts/ttf
Then I had to delete fontList.cache file for the new font to be loaded.
rm ~/.cache/matplotlib/fontList.cache
Note
You can have different views by changing the input to the draw_networkx e.g. not sending the linewidths will show circular border for each node, also if you want a specific background color for nodes change the color_node from white to a color that you want ... for more details check the documentation.