sl.writeSBMLFile("ftest_layout_override.xml") # This will write if allowed, and when it is read back in, it displays as # a single blob of garbage because everything is plotted with the same centers # sl.writeSBMLFile("test_layout_override.xml") # slr = SBMLlayout("test_layout_override.xml", autoComputeLayout=False) slr = SBMLlayout(str(model_file), autoComputeLayout=False) slr._describeModel() slr.drawNetwork() assert slr.getNodeTextAnchor("MKK_P") == "center" # bottom means top in this situation assert slr.getNodeVTextAnchor("MAPK") == "bottom" assert slr.getNodeFontSize("MKK") == 11 assert slr.getNodeEdgeColor("MKKK") == "#969696" assert slr.getNodeFillColor("MAPK_P") == "#c9e0fb" assert slr.getReactionEdgeColor("J1") == [('MKKK_P', 'SUBSTRATE', '#ff9900'), ('MKKK', 'PRODUCT', '#ff9900')] assert slr.getReactionFillColor("J2") == [('MKK', 'SUBSTRATE', '#ff9900'), ('MKK_P', 'PRODUCT', '#ff9900'), ('MKKK_P', 'ACTIVATOR', '#ff9900')]
assert sl.getNodeVTextAnchor("pyruvate") == "bottom" assert sl.getNodeVTextAnchor("ADP") == "bottom" assert sl.getNodeFillColor("NAD") == "#7fff55" assert sl.getNodeFillColor("NADH") == "#d4ffaa" assert sl.getNodeFillColor("ATP") == "#ff7faa" assert sl.getNodeFillColor("ADP") == "#ffd4d4" assert sl.getNodeEdgeColor("glycerate_3_phosphate") == "#969696" sl.writeSBMLFile("glycolysis_original.xml") slr = SBMLlayout("glycolysis_original.xml") slr.drawNetwork() assert slr.getNumberOfNodes() == 23 assert slr.getNumberOfReactions() == 11 assert slr.getReactionCurveWidth("J9") == [('ATP', 'SUBSTRATE', 2.0), ('ADP', 'PRODUCT', 2.0)] assert slr.getReactionEdgeColor("J10") == [('External_acetaldehyde', 'SUBSTRATE', '#ff9900'), ('Sink', 'PRODUCT', '#ff9900')] assert slr.getReactionFillColor("J0") == [('External_glucose', 'SUBSTRATE', '#ff9900'), ('Glucose', 'PRODUCT', '#ff9900')]
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")) sl.drawNetwork() sl.showLayoutAlgorithmOptions() #sl.setLayoutAlgorithm_grav(20) sl.setLayoutAlgorithmOptions(k=40, grav=20) #sl.setLayoutAlgorithmOptions(mag=1) sl.showLayoutAlgorithmOptions() sl.regenerateLayout()
assert sl.getNodeFontSize("ABCDEFG") == 12 assert sl.getNodeFontWeight("F") == "normal" assert sl.getNodeFillColor("E") == "#a0e0a030" sl.drawNetwork("larger_pathway.png") # sl.setReactionCurveWidth("all", 12) sl.drawNetwork() sl.writeSBMLFile("ftest_larger_pathway.xml") slr = SBMLlayout("ftest_larger_pathway.xml") slr.drawNetwork() assert sl.getNumberOfNodes() == 6 assert sl.getNumberOfReactions() == 5 assert sl.getReactionCurveWidth("_J2") == [('C', 'SUBSTRATE', 3.0), ('ABCDEFG', 'PRODUCT', 3.0)] assert sl.getReactionEdgeColor("_J1") == [('B', 'SUBSTRATE', '#000000a0'), ('C', 'PRODUCT', '#000000a0'), ('D', 'PRODUCT', '#000000a0')]
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")) print("_J3 edge color: ", sl.getReactionEdgeColor("_J3")) print("_J3 fill color: ", sl.getReactionFillColor("_J3")) print("_J4 edge color: ", sl.getReactionEdgeColor("_J4")) print("_J4 fill color: ", sl.getReactionFillColor("_J4")) print("A: fill color: ", sl.getNodeFillColor("A")) print("B: edge color: ", sl.getNodeEdgeColor("B")) print("C: edge width: ", sl.getNodeEdgeWidth("C")) print("X0: text anchor: ", sl.getNodeTextAnchor("X0")) print("A: text anchor: ", sl.getNodeTextAnchor("A")) print("B: vtext anchor: ", sl.getNodeVTextAnchor("B"))
assert sl.getNodeEdgeColor("A") == "#0000ff" assert sl.getNodeFillColor("A") == "#c9e0fb" sl.setNodeFontWeight(["A", "B", "C", "D"], "bold") assert sl.getNodeFontWeight("B") == "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") assert sl.getReactionEdgeColor("_J0")[0] == ('X0', 'SUBSTRATE', '#0000ff') assert sl.getReactionEdgeColor("_J0")[1] == ('A', 'PRODUCT', '#ff0000ff') assert sl.getReactionEdgeColor("_J1")[0] == ("A", "SUBSTRATE", "#ff00ffff") assert sl.getReactionEdgeColor("_J1")[1] == ("B", "PRODUCT", "#0000ff") assert sl.getReactionEdgeColor("_J2")[0] == ('B', 'SUBSTRATE', '#0000ff') assert sl.getReactionEdgeColor("_J2")[1] == ('D', 'PRODUCT', '#ff00ffff') assert sl.getReactionEdgeColor("_J5")[0] == ('D', 'SUBSTRATE', '#00ff00ff') assert sl.getReactionEdgeColor("_J5")[1] == ('X1', 'PRODUCT', '#0000ff') assert sl.getReactionEdgeColor("_J3")[0] == ('A', 'SUBSTRATE', '#0000ff') assert sl.getReactionEdgeColor("_J3")[1] == ('C', 'PRODUCT', '#ffff00ff') assert sl.getReactionEdgeColor("_J4")[0] == ('C', 'SUBSTRATE', '#00ffffff')