else:
model_dir = "/Users/natalieh/repos/libsbml-draw/model_files/"
model_file = "/Users/natalieh/repos/libsbml-draw/model_files/copasi.xml"
#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"
Gradient colours are cool. Would like to see them.
Font size should scale with scaling factor
'''
layout = SBMLlayout('Kholodenko2000.xml')
# print(layout.getNumberOfRoles())
layout.regenerateLayout()
[layout.setCompartmentEdgeColor(i, 'grey') for i in layout.getCompartmentIds()]
[layout.setNodeEdgeWidth(i, 10) for i in layout.getNodeIds()]
[layout.setNodeFontSize(i, 40) for i in layout.getNodeIds()]
[layout.setCompartmentLineWidth(i, 25) for i in layout.getCompartmentIds()]
# [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('Kholodenko2000Layout.png', scaling_factor=1.5)
# 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
sl = SBMLlayout(model_file)
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",
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()
