sl._describeModel() sl.drawNetwork() #r = Render(model_file, sl.layout_number) #r._describeRenderInfo() #print("render: ", type(r)) #print("num layouts: ", r.layout_plugin.getNumLayouts()) #sl._applyRenderInformation(None) #a0e0a030 reactionIds = sl.getReactionIds() sl.setNodeColor("all", "#0000ff30") sl.setReactionColor("all", "blue") sl.setNodeEdgeColor("F", "blue") sl.setNodeFillColor("F", "lightgreen") sl.setNodeFontFamily("ABCDEFG", "Elephant") sl.setNodeFontColor("ABCDEFG", "green") sl.setNodeEdgeColor("ABCDEFG", "blue") for reactionId in reactionIds: sl.setReactionCurveWidth(reactionId, 1) sl.setReactionFillColor(reactionId, "red") sl.drawNetwork(save_file_name="C:\\tmp\\larger_pathway_set_changes_tight.png", bbox_inches="tight")
#model_file = Path(pkg_resources.resource_filename("libsbml_draw", "model_files/model.xml")) print("model file: \n", model_file) sl = SBMLlayout(model_file) sl._describeModel() ## Draw Original copasi.xml sl.drawNetwork() print("node ids: ", sl.getNodeIds()) print("reaction ids: ", sl.getReactionIds()) sl.setNodeFontStyle("S1", "italic") sl.setNodeColor("S1", "lightpink") sl.setNodeColor("S2", "lightgreen") sl.setNodeFontColor("S1", "white") sl.setNodeFontStyle("S1", "italic") sl.setReactionColor("_J0", "blue") sl.setReactionCurveWidth("_J0", 1) # Draw Pink and Green sl.drawNetwork() new_model_file = model_dir + "render_sbml_pink_green.xml" print("new model file: ", new_model_file) sl.addRenderInformation()
# describe network print("num nodes: ", sl.getNumberOfNodes()) print("num reactions: ", sl.getNumberOfReactions()) # create network sl._createNetwork() # draw network sl.drawNetwork() # print node id's print("node ids: ", sl.getNodeIds()) if "copasi" in model_file: # set node properties sl.setNodeColor("S1", "pink") sl.setNodeColor("S2", "green") sl.setNodeColor("S1", "Verdana") sl.setNodeColor("S1", "white") sl.setNodeFontsize("S1", 18) sl.setNodeFontstyle("S1", "italic") sl.setNodeFontsize("S2", 24) sl.setNodeFontstyle("S2", "oblique") sl.setNodeFontcolor("S2", "yellow") # print reaction id's print("reaction ids: ", sl.getReactionIds()) #sl.setReactionColor("_J0", "orange") #sl.setReactionCurveWidth("_J0", 5)
from pathlib import Path import pkg_resources from libsbml_draw.model.sbml_layout import SBMLlayout model_file_name = "model.xml" model_file = Path( pkg_resources.resource_filename("libsbml_draw", "model/data/" + model_file_name)) s = SBMLlayout(str(model_file)) # s._describeModel() s.setNodeFontSize('all', 15) s.setReactionCurveWidth('all', 3) s.setNodeColor('all', 'red') s.setNodeFontColor('all', 'white') s.drawNetwork() s.regenerateLayout() s.drawNetwork()
sl2.drawNetwork() sl.getArrowheadVert(1, 1) centroid = sl.getNodeCentroid("X0") print("centroid: ", centroid) centroid = sl.getReactionCentroid("_J0") print("rxn centroid: ", centroid) #centroid = sl.getReactionCentroid("J0") #print("rxn centroid: ", centroid) print("X0", sl.getNodeColor("X0")) #print("X", sl.getNodeColor("X")) sl.setNodeColor("all", "lightpink") sl.setNodeEdgeColor("all", "purple") sl.setNodeEdgeColor("X0", "green") sl.setNodeFillColor("X0", "yellow") sl.setNodeEdgeWidth("all", 2) sl.setNodeEdgeWidth("X1", 5) sl.setNodeEdgeWidth(["A", "B", "C"], 3) sl.setReactionCurveWidth("_J0", 3) sl.setReactionColor("all", "purple") sl.setReactionColor("_J0", "green") # KeyError in setter #sl.setReactionColor("_J", "green") # ValueError in matplotlib #sl.setReactionColor("_J1", "greene")
model_file_name = "model.xml" model_file = Path( pkg_resources.resource_filename("libsbml_draw", "model/data/" + model_file_name)) applyRender = True sl = SBMLlayout(str(model_file), applyRender=applyRender) sl.lockNode("X0") sl.lockNode("A") sl.aliasNode("B") sl.setNodeColor("B_1", "#00ff0030") sl.setNodeColor("A", "#00ff0030") sl.lockNode("B_1") sl.lockNode("D") sl.unlockNode("X0") sl.unlockNode("A") def test_node_locking(): assert sl.getIsNodeLocked("D") == True assert sl.getIsNodeLocked("B_1") == True assert sl.getIsNodeLocked("X0") == False assert sl.getIsNodeLocked("A") == False assert sl.getIsNodeLocked("C") == False
layout.regenerateLayout() layout.regenerateLayout() layout.regenerateLayout() layout.regenerateLayout() layout.regenerateLayout() [layout.setCompartmentEdgeColor(i, 'grey') for i in layout.getCompartmentIds()] [layout.setCompartmentLineWidth(i, 10) for i in layout.getCompartmentIds()] [layout.setNodeEdgeWidth(i, 10) for i in layout.getNodeIds()] [layout.setNodeFontSize(i, 40) for i in layout.getNodeIds()] [ layout.setReactionEdgeColor(i, edge_color='black') for i in layout.getReactionIds() ] [layout.setReactionCurveWidth(i, 10) for i in layout.getReactionIds()] [layout.setArrowheadScale(i, 50) for i in range(layout.getNumberOfRoles())] [layout.setNodeColor(i, 'white') for i in layout.getNodeIds()] [layout.setNodeEdgeColor(i, 'black') for i in layout.getNodeIds()] layout.drawNetwork('compartment_network.png') # layout.regenerateLayout() # layout.regenerateLayout() # layout.regenerateLayout() # layout.regenerateLayout() # layout.regenerateLayout() # layout.drawNetwork('compartment_network.png') # # layout.writeSBMLFile('2CompartmentModelWithLayout.xml') # # from libsbml_draw.model.sbml_layout import SBMLlayout # # # Create a SBMLlayout object.