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))
