I have taken an initial DOT file and modified the pos attributes of some nodes using pydot. Now I want to render an image file that shows the nodes in their new positions. The catch is, I don't want a layout program to mess with the positions! I just want to see the nodes exactly where the pos attribute indicates. I don't care about how the edges look.
I can produce a DOT file with my positions easily using pydot, but I can't figure out how to make an image file, either in pydot or on the command line with dot. Help would be really appreciated! Thanks!
dot.write_png('filename.png')? Or is there something I'm missing?
Also, the neato command-line program has a -n option for graph files that already have layout. The program description says it is for undirected graphs, but I tried it with a digraph and it produced the correct result.
Related
I am converting my networkx graph using the following code.
nx.drawing.nx_pydot.write_dot(G,path)
It creates a correct dot format which I can visualize later using graphviz interface. However, instead of adding multiple existing lines(Arcs, edges whatever you say), it creates a single (or two if there is an edge in the opposite direction). I just want to have all lines to be preserved in the dot format. How can I do that?
The creation of Networkx graph in the first place was not correct. I changed the line G=nx.DiGraph(directed=True) to G=nx.MultiDiGraph(directed=True). Now I do not have that problem.
I am creating a graph using python and graphviz.
So my script goes like :
from graphviz import Digraph
dot = Digraph()
dot.node('Start')
dot.node('Calculate A')
dot.edge('Start', 'Calculate A')
and so on.
I need to write math text in some nodes, let's say, replace 'A' by an integral. How can that be done?
Thanks in advance,
M
Sorry, Graphviz does not support LaTeX.
In theory, you could use Unicode & Graphviz (pseudo) HTML to create what you want, but it would probably be quite challenging.
A (pretty) easy way to combine LaTex and Graphviz would be to create separate image files (svg, png, jpeg, ...) - one per node using your "usual" LaTeX processes and then "including" these files in your Graphviz program using the image attribute.
I am using python module for pydot to make flowcharts. But the flowcharts are being generated in a vertical fashion. I want them to be generated in a horizontal way. Is there any way that this can be achieved?
You need to give your graph the rankdir=LR attribute, as shown in this Graphviz forum post.
I don't know pydot (but I have written a few programs that create graphs in the DOT language), so I don't know the exact syntax you need to use, and I'm having trouble locating docs for pydot, but it appears that you can just pass the attribute as a keyword in the Dot constructor, eg
dot_object = pydot.Dot(graph_name="main_graph", rankdir="LR", ...)
I'm trying to use Python to plot simple hierarchical tree. I'm using the networkx module. I declared a simple graph
G=networkx.DiGraph()
After adding nodes and edges into G, I tried using
nx.draw(G)
or
nx.draw_networkx(G)
to plot. The output plot hierarchy are all correct, but the position of the nodes appears all random on the graph. Even worse, each time I ran the script, the node position are different.
There is a solution provided in a similar question which requires graphviz package.
pos=nx.graphviz_layout(G,prog='dot')
nx.draw(G,pos,with_labels=False,arrows=False)
Unfortunately I'm not allowed to install graphviz. So I'm seeking alternative solution here.
From graphviz solution, it looks like it's only needed to compute position of the node. Is it correct to say that, as long as I specify a list of coordinates to the draw command, I would be able to plot node at the correct location?
Thanks
UPDATE (15 Apr 2015) Look at my answer here for code that I think will do what you're after.
So networkx doesn't make it particularly easy to use the graphviz layout if you don't have graphviz because it's a better idea to use graphviz's algorithm if you're trying to reproduce graphviz's layout.
But, if you're willing to put in the effort to calculate the position for each node this is straightforward (as you guessed). Create a dict saying where each node's position should be.
pos = {}
for node in G.nodes():
pos[node] = (xcoord,ycoord)
nx.draw(G,pos)
will do it where xcoord and ycoord are the coordinates you want to have.
The various plotting commands are described here
I wrote a python class to display and animate binary search trees. Yet the graphs produced by the pyDot edge and node commands don't seem to allow me to control the angle or direction of the arrows connecting each element of my tree.
There are lots of controls for shape of the nodes but there does not seem to be any control for angle of the lines. I was hoping to find some kind of minimum angle parameter to add to my edges as they are added to the graph?
This is a sample of my code where I draw nodes using the edge command:
def draw(parent_name, child_name):
# color for lines = red
edge = pydot.Edge(parent_name, child_name, color="#ff0000")
graph.add_edge(edge)
The end result is that my graphs for binary search trees don't look like the traditional tree structures when several nodes have only one child.
Here is a link to my project where you can see the otherwise working results:
http://www.embeddedcomponents.com/blogs/2013/12/visualizing-software-tree-structures/
from pydot documentation:
create will write the graph to a temporary dot file and process
it with the program given by 'prog' (which defaults to 'twopi'),
reading the Postscript output and returning it as a string is the
operation is successful.
it is not possible to directly control edges angels using the dot language, but adding invisible edges can give you the result you want, see an example here that generates the following graph: