Hi,
This won't help with the actual laying out of the graph (as in, I assume
networkX can decide the "best" x,y coordinates of the nodes) but pyqtgraph
has the GraphItem, which can render a graph network. I'm not sure how you'd
go about obtaining the node positions etc from networkX and passing them to
the pyqtgraph, but it might be possible to make a bridge between them
somehow. Or yeah, get NetworkX to dump out data in some easy format and
read it back in and recreate the graph in pyqtgraph.
Have you seen the "Labeled Graph" demo in the examples?
(https://github.com/pyqtgraph/pyqtgraph/blob/develop/examples/CustomGraphItem.py)
Not sure if that will help or not -- apologies I don't have any experience
with NetworkX or plotting graphs in pyqtgraph...
With the matplotlib widget, as far as I'm aware it's just a simple wrapper
around a matplotlib figure as a QWidget. I don't think it will give you any
additional benefits of just plotting in matplotlib.
Patrick
On Friday, 17 August 2018 06:48:28 UTC+9:30, JME wrote:
>
> I have been attempting to plot a network, generated from networkX, in a
> pyqtgraph widget. NetworkX generates graphs for Matplotlib (and by that, I
> mean...it plots...not well, and not interactive), and I was hoping to be
> able to use pyqtgraph to display these graphs. Since they are not
> coordinate based figures, however, I believe that there are some problems
> passing the network to the plotting functions. I can use networkX to
> generate [and save] things like .graphML , GEXF, GML,YAML,SparseGraph6,
> Pajek, and so on, but is there a way to then plot or open these datatypes
> in a pyqtgraph widget to be able to "zoom around" and look at them?
> I thought about using the matplotlib widget within the pyqtgraph plot, but
> I don't know what this entails, or if it has any added value to just using
> a matplotlib canvas anyways.
>
> To make the matplotlib widget, I use the following:
>
> from PyQt5 import QtWidgets
> from matplotlib.figure import Figure
> from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as Canvas
> import matplotlib
>
> # Ensure using PyQt5 backend
> matplotlib.use('QT5Agg')
>
> # Matplotlib canvas class to create figure
> class MplCanvas(Canvas):
> def __init__(self):
> self.fig = Figure()
> self.ax = self.fig.add_subplot(111)
> self.ax.cla()#test
> Canvas.__init__(self, self.fig)
> Canvas.setSizePolicy(self, QtWidgets.QSizePolicy.Expanding,
> QtWidgets.QSizePolicy.Expanding)
> Canvas.updateGeometry(self)
>
> # Matplotlib widget
> class MplWidget(QtWidgets.QWidget):
> def __init__(self, parent=None):
> QtWidgets.QWidget.__init__(self, parent) # Inherit from QWidget
> self.canvas = MplCanvas() # Create canvas object
> self.vbl = QtWidgets.QVBoxLayout() # Set box for plotting
> self.vbl.addWidget(self.canvas)
> self.setLayout(self.vbl)
>
>
>
>
> To generate the network in the Matplotlib widget, I do the following:
>
> G = nx.Graph()#create a networkx graph
> Comparison_List = pd.read_csv("SampleTracker.csv",index_col=[0])
> #just some data filtering for the next few steps
> Comparison_List2 =
> Comparison_List[Comparison_List["Status"]=='Finalized'].Sample_ID.tolist()
> Comparison_List3 =
> Comparison_List[Comparison_List["Status"]=='Data Processing
> Needed'].Sample_ID.tolist()
> fulledgelist=[]
> for i in obj_Network.index.tolist():
> edgelist = eval(obj_Network.loc[i]["Trait_1"])
> if len(edgelist) < len(Comparison_List2):
> edgelist_condensed = edgelist
> for y in edgelist_condensed:
> Value = (i,y)
> fulledgelist.append(Value)
> goldlist = [item for item in fulledgelist]
> G.add_nodes_from(obj_Network.index.tolist(),color='yellow') #Add
> nodes
> G.add_nodes_from(Comparison_List2,color='green')
> G.add_nodes_from(Comparison_List3,color='orange')
> G.add_edges_from(goldlist,weight=0.8) #connect the nodes
> nx.draw_spring(G, with_labels=True,ax=self.widget.canvas.ax)#Altered
> to display on ax axis
> self.widget.canvas.draw() #this works as an MPL.pyplot object
> (with correct back-ends enabled)
>
> I believe the problem is the final part, where the "canvas" is a mpl
> object. Whereas, the pyqtgraph function obviously does not know how to
> handle the request to "draw".
>
> Any thoughts or ideas? Thanks for your time.
>
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