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")
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") print("reaction edge: ", sl.getReactionEdgeColor("_J0")) print("reaction fill: ", sl.getReactionFillColor("_J0"))
#sl2.writeSBMLFile("model_out_render.xml") sl.setReactionColor("_J0", "red", species="A") sl.setReactionEdgeColor("_J3", "#0000ff30") sl.setReactionEdgeColor("_J4", "pink", species="D") # only applies to FancyArrowPatch arrowhead sl.setReactionFillColor("_J2", "lightgreen") sl.setReactionCurveWidth("_J0", 5, role_name="product") sl.setReactionCurveWidth("_J4", 10) sl.setReactionCurveWidth(["_J1", "_J2", "_J3"], 15) sl.setNodeFillColor("A", "pink") sl.setNodeEdgeColor("all", "green") sl.setNodeEdgeWidth(["D", "X1", "C"], 3) sl.setNodeFontWeight(["X0", "A", "B", "C", "D", "X1"], "bold") sl.setNodeTextAnchor("X0", "right") sl.setNodeTextAnchor("A", "left") sl.setNodeVTextAnchor("B", "center") sl.drawNetwork() print("_J0 width: ", sl.getReactionCurveWidth("_J0")) print("_J1 edge color: ", sl.getReactionEdgeColor("_J1")) print("_J1 fill color: ", sl.getReactionFillColor("_J1"))
if platform.system() == "Windows": model_dir = "C:\\Users\\nrhaw\\Documents\\repos\\libsbml-draw\\model_files\\" elif platform.system() == "Linux": model_dir = "/home/radix/repos/libsbml-draw/model_files/" else: model_dir = "/Users/natalieh/repos/libsbml-draw/model_files/" model_file = model_dir + file_name print("model file: \n", model_file) sl = SBMLlayout(model_file) sl._describeModel() my_fig = sl.drawNetwork() color1 = ["S6", "S7", "S5", "S4", "S8"] color2 = ["S0", "S1", "S2", "S3", "S9", "S10", "S11"] for node in color1: sl.setNodeFillColor(node, "lightblue") for node in color2: sl.setNodeFillColor(node, "lightgreen") for reaction in sl.getReactionIds(): sl.setReactionCurveWidth(reaction, 2) sl.drawNetwork()
model_file = Path( pkg_resources.resource_filename("libsbml_draw", "model/data/" + model_file_name)) applyRender = True sl = SBMLlayout(str(model_file), applyRender=applyRender) sl._describeModel() sl.setReactionCurveWidth("all", 5) sl.setReactionCurveWidth("_J0", 7, role_name="product") sl.setNodeEdgeColor("X1", "#ff0000") sl.setNodeFillColor("X1", "#ff000030") sl.setNodeEdgeWidth("X1", 3) sl.setNodeFontWeight(["A", "B", "C", "D"], "bold") sl.setReactionEdgeColor("_J0", "#ff0000", role_name="product") sl.setReactionEdgeColor("_J1", "#ff00ff", role_name="substrate") sl.setReactionEdgeColor("_J2", "#ff00ff", role_name="product") sl.setReactionEdgeColor("_J5", "#00ff00", species="D") sl.setReactionEdgeColor("_J3", "#ffff00", role_name="product") sl.setReactionEdgeColor("_J4", "#00ffff") model_file_name = "ftest_no_layout.xml" model_file = Path( pkg_resources.resource_filename("libsbml_draw", "model/data/" + model_file_name))