def createHeatmap(graph, distanceGraph, timePoint):
if graph.getSubGraph("heatmap") != None:
heatmap = graph.getSubGraph("heatmap")
graph.delSubGraph(heatmap)
heatmap = graph.addCloneSubGraph("heatmap")
heatmap.clear()
tlp.copyToGraph(heatmap, distanceGraph)
expression_lvl = heatmap.getDoubleProperty("Expression_lvl")
tps = heatmap.getDoubleProperty("Tps")
Locus = heatmap.getStringProperty("Locus")
groupesHeatmap = heatmap.getDoubleProperty('resultMetric1')
groupes = distanceGraph.getDoubleProperty('resultMetric1')
for n in heatmap.getEdges():
heatmap.delEdge(n)
nodesListe = []
#for n in heatmap.getNodes():
count = 0
for n in heatmap.getNodes():
count = count + 1
nodesListe.append(n)
for n in nodesListe:
expression_lvl[n] = timePoint[0][n]
tps[n] = 1
addedNodes = heatmap.addNodes(17)
tps = heatmap.getDoubleProperty("Tps")
for m in range(len(addedNodes)):
expression_lvl[addedNodes[m]] = timePoint[m][n]
tps[addedNodes[m]] = m + 1
Locus[addedNodes[m]] = Locus[n]
groupesHeatmap[addedNodes[m]] = groupesHeatmap[n]
for n in nodesListe:
heatmap.delNode(n)
return heatmap
def createCleanCopy(graph, graph_to_copy, copy_name):
copy = graph.addCloneSubGraph(copy_name)
copy.clear()
tlp.copyToGraph(copy, graph_to_copy)
return copy
def import_from_query():
"""Use the query drawer plugin to draw the built query"""
params = tlp.getDefaultPluginParameters("QueryDrawer")
params['Query'] = query.get()
params['URI'] = self.dataSet['URI']
params["User name"] = self.dataSet["User name"]
params["Password"] = self.dataSet["Password"]
params["Directory path"] = self.dataSet["Directory path"]
tlp.copyToGraph(self.graph, tlp.importGraph("QueryDrawer", params))
root.destroy()
def reinitializeSubgraph(graph, name, clone_name="clone"):
if graph.getSubGraph(name) is None:
print("creation of {} subGraph".format(name))
sub = graph.addCloneSubGraph(name)
else:
sub = graph.getSubGraph(name)
sub.clear()
clone = graph.getSubGraph(clone_name)
tlp.copyToGraph(sub, clone)
return sub
def createSmallMultiples(g, timelapse):
smallMultiples = g.addSubGraph("smallMultiples")
list_node = []
gInteract = g.getSubGraph("Genes interactions")
for n in gInteract.getNodes():
list_node.append(n)
i = 1
for lapse in timelapse:
name = "tp " + str(i)
tp = smallMultiples.addSubGraph(name)
tlp.copyToGraph(tp, gInteract)
metricTP = tp.getDoubleProperty("viewMetric")
for node in tp.getNodes():
metricTP[node] = lapse[node]
i += 1
def buildSmallMultiples(smallMultiplesTree, geneInteractions, timepoints,
metric):
for i in range(1, len(timepoints) + 1):
tp = smallMultiplesTree.addSubGraph("tp" + str(i) + " s")
inGraph = graph.getSubGraph("Genes interactions")
tlp.copyToGraph(tp, inGraph, inSelection=None, outSelection=None)
for time in timepoints:
for sg in smallMultiplesTree.getSubGraphs():
metric = sg.getLocalDoubleProperty("viewMetric")
for n in sg.getNodes():
timePropertyName = str(time).split(" ")
timeName = timePropertyName[2] + " s"
#Check if the name of the graph (associated to one timepoint) is equal to the right timepoint property
if (timeName == sg.getName()):
metric[n] = time[n]
def createHeatmap(graph, distanceGraph, timePoint):
'''
Crée une Heatmap en fonction des niveaux d'expression des gènes.
Dans ce sous-graphe, chaque gène est présent en 17 exemplaire, un par pas de temps.
'''
if graph.getSubGraph("heatmap") != None:
heatmap = graph.getSubGraph("heatmap")
graph.delSubGraph(heatmap)
heatmap = graph.addCloneSubGraph("heatmap")
heatmap.clear()
tlp.copyToGraph(heatmap, distanceGraph)
expression_lvl = heatmap.getDoubleProperty("Expression_lvl")
tps = heatmap.getDoubleProperty("Tps")
Locus = heatmap.getStringProperty("Locus")
groupesHeatmap = heatmap.getDoubleProperty('cluster1')
groupes = distanceGraph.getDoubleProperty('cluster1')
for n in heatmap.getEdges():
heatmap.delEdge(n)
nodesListe = []
count = 0
for n in heatmap.getNodes():
count = count + 1
nodesListe.append(n)
for n in nodesListe:
expression_lvl[n] = timePoint[0][n]
tps[n] = 1
addedNodes = heatmap.addNodes(17)
tps = heatmap.getDoubleProperty("Tps")
for m in range(len(addedNodes)):
expression_lvl[addedNodes[m]] = timePoint[m][n]
tps[addedNodes[m]] = m + 1
Locus[addedNodes[m]] = Locus[n]
groupesHeatmap[addedNodes[m]] = groupesHeatmap[n]
for n in nodesListe:
heatmap.delNode(n)
return heatmap
def createHierarchy(smallMultGraph, interactGraph, rootGraph):
""" Function to create a subgraphes hierarchy into the small multiple graph, which is a subragraph of the root graph.
Each subgraph of the small multiple graph represents the gene interaction graph at a specific time point. The values
of this time point will be stored in the double property of the subgraph "viewMetric".
Args:
smallMultGraph (tlp.Graph) : the small multiple graph
interactGraph (tlp.Graph) : the gene interaction graph
rootGraph (tlp.Graph) : the root graph of the project
Returns:
None
"""
listNodes = []
for index in range(1, 18):
tp_i = rootGraph.getLocalDoubleProperty("tp{} s".format(index))
subCopyGraph = smallMultGraph.addSubGraph("tp{}".format(index))
tlp.copyToGraph(subCopyGraph, interactGraph)
metric = subCopyGraph.getLocalDoubleProperty("viewMetric")
tp_i = rootGraph.getDoubleProperty("tp{} s".format(index))
metric.copy(tp_i)
colorSmallMultiples(subCopyGraph, metric)
def draw_timePoint_hierarchy(TPs, SM, gene):
"""
Add a Small Multiples subgraph for each time points with the genes interractions properties.
Time points data are set in the viewMetric columns and defined the graph colors.
@type TPs: list
@param TPs: the Time points name
@type SM: Tulip graph
@param SM: Small Multiples subgraph
@type gene: Tulip graph
@param gene: Genes interactions subgraph
"""
viewColor = graph.getColorProperty("viewColor")
for tp in TPs:
tmp = SM.addSubGraph(tp)
tlp.copyToGraph(tmp, gene)
Metric = tmp.getDoubleProperty("viewMetric")
pr = tmp.getDoubleProperty(tp)
for n in tmp.getNodes():
properties = tmp.getNodePropertiesValues(n)
Metric[n] = properties[tp]
color_graph(tmp, pr, viewColor)
def main(graph):
#
if graph.getSubGraph("Clone") == None:
clone = graph.addCloneSubGraph("Clone")
else:
clone = graph.getSubGraph("Clone")
if graph.getSubGraph("Working") == None:
working = graph.addCloneSubGraph("Working")
else:
working = graph.getSubGraph("Working")
working.clear(
) #A commenter si le projet est déjà chargé et l'on souhaite éviter de tout relancer
tlp.copyToGraph(
working, clone
) #A commenter si le projet est déjà chargé et l'on souhaite éviter de tout relancer
Locus = working.getStringProperty("Locus")
Negative = working.getBooleanProperty("Negative")
Positive = working.getBooleanProperty("Positive")
tp1_s = working.getDoubleProperty("tp1 s")
tp10_s = working.getDoubleProperty("tp10 s")
tp11_s = working.getDoubleProperty("tp11 s")
tp12_s = working.getDoubleProperty("tp12 s")
tp13_s = working.getDoubleProperty("tp13 s")
tp14_s = working.getDoubleProperty("tp14 s")
tp15_s = working.getDoubleProperty("tp15 s")
tp16_s = working.getDoubleProperty("tp16 s")
tp17_s = working.getDoubleProperty("tp17 s")
tp2_s = working.getDoubleProperty("tp2 s")
tp3_s = working.getDoubleProperty("tp3 s")
tp4_s = working.getDoubleProperty("tp4 s")
tp5_s = working.getDoubleProperty("tp5 s")
tp6_s = working.getDoubleProperty("tp6 s")
tp7_s = working.getDoubleProperty("tp7 s")
tp8_s = working.getDoubleProperty("tp8 s")
tp9_s = working.getDoubleProperty("tp9 s")
viewBorderColor = working.getColorProperty("viewBorderColor")
viewBorderWidth = working.getDoubleProperty("viewBorderWidth")
viewColor = working.getColorProperty("viewColor")
viewFont = working.getStringProperty("viewFont")
viewFontSize = working.getIntegerProperty("viewFontSize")
viewIcon = working.getStringProperty("viewIcon")
viewLabel = working.getStringProperty("viewLabel")
viewLabelBorderColor = working.getColorProperty("viewLabelBorderColor")
viewLabelBorderWidth = working.getDoubleProperty("viewLabelBorderWidth")
viewLabelColor = working.getColorProperty("viewLabelColor")
viewLabelPosition = working.getIntegerProperty("viewLabelPosition")
viewLayout = working.getLayoutProperty("viewLayout")
viewMetric = working.getDoubleProperty("viewMetric")
viewRotation = working.getDoubleProperty("viewRotation")
viewSelection = working.getBooleanProperty("viewSelection")
viewShape = working.getIntegerProperty("viewShape")
viewSize = working.getSizeProperty("viewSize")
viewSrcAnchorShape = working.getIntegerProperty("viewSrcAnchorShape")
viewSrcAnchorSize = working.getSizeProperty("viewSrcAnchorSize")
viewTexture = working.getStringProperty("viewTexture")
viewTgtAnchorShape = working.getIntegerProperty("viewTgtAnchorShape")
viewTgtAnchorSize = working.getSizeProperty("viewTgtAnchorSize")
timePoint = [
tp1_s, tp2_s, tp3_s, tp4_s, tp5_s, tp6_s, tp7_s, tp8_s, tp9_s, tp10_s,
tp11_s, tp12_s, tp13_s, tp14_s, tp15_s, tp16_s, tp17_s
]
pretraitement(working, Locus, Negative, Positive, viewColor, viewLabel,
viewLayout, viewSize)
applyModelForce(working, viewLayout)
distanceGraph = createDistanceGraph(working)
maxDepth = 3
partitionnement(distanceGraph, maxDepth)
heatmap = createHeatmap(working, distanceGraph, timePoint)
#heatmap = working.getSubGraph("heatmap")
colorHeatmap(heatmap)
construireGrille(distanceGraph, heatmap)
#clone=graph.getSubGraph("Clone")
regulateurs = trouverRegulateur(clone)
trouverRegule(clone, regulateurs)
saveClusters(distanceGraph, 0.0)
saveClusters(distanceGraph, 1.0)
def main(graph):
#
if graph.getSubGraph("Clone") == None:
clone = graph.addCloneSubGraph("Clone")
else:
clone = graph.getSubGraph("Clone")
if graph.getSubGraph("Working") == None:
working = graph.addCloneSubGraph("Working")
else:
working = graph.getSubGraph("Working")
working.clear()
tlp.copyToGraph(working, clone)
# working = graph.getSubGraph("Working")
Locus = working.getStringProperty("Locus")
Negative = working.getBooleanProperty("Negative")
Positive = working.getBooleanProperty("Positive")
tp1_s = working.getDoubleProperty("tp1 s")
tp10_s = working.getDoubleProperty("tp10 s")
tp11_s = working.getDoubleProperty("tp11 s")
tp12_s = working.getDoubleProperty("tp12 s")
tp13_s = working.getDoubleProperty("tp13 s")
tp14_s = working.getDoubleProperty("tp14 s")
tp15_s = working.getDoubleProperty("tp15 s")
tp16_s = working.getDoubleProperty("tp16 s")
tp17_s = working.getDoubleProperty("tp17 s")
tp2_s = working.getDoubleProperty("tp2 s")
tp3_s = working.getDoubleProperty("tp3 s")
tp4_s = working.getDoubleProperty("tp4 s")
tp5_s = working.getDoubleProperty("tp5 s")
tp6_s = working.getDoubleProperty("tp6 s")
tp7_s = working.getDoubleProperty("tp7 s")
tp8_s = working.getDoubleProperty("tp8 s")
tp9_s = working.getDoubleProperty("tp9 s")
viewBorderColor = working.getColorProperty("viewBorderColor")
viewBorderWidth = working.getDoubleProperty("viewBorderWidth")
viewColor = working.getColorProperty("viewColor")
viewFont = working.getStringProperty("viewFont")
viewFontSize = working.getIntegerProperty("viewFontSize")
viewIcon = working.getStringProperty("viewIcon")
viewLabel = working.getStringProperty("viewLabel")
viewLabelBorderColor = working.getColorProperty("viewLabelBorderColor")
viewLabelBorderWidth = working.getDoubleProperty("viewLabelBorderWidth")
viewLabelColor = working.getColorProperty("viewLabelColor")
viewLabelPosition = working.getIntegerProperty("viewLabelPosition")
viewLayout = working.getLayoutProperty("viewLayout")
viewMetric = working.getDoubleProperty("viewMetric")
viewRotation = working.getDoubleProperty("viewRotation")
viewSelection = working.getBooleanProperty("viewSelection")
viewShape = working.getIntegerProperty("viewShape")
viewSize = working.getSizeProperty("viewSize")
viewSrcAnchorShape = working.getIntegerProperty("viewSrcAnchorShape")
viewSrcAnchorSize = working.getSizeProperty("viewSrcAnchorSize")
viewTexture = working.getStringProperty("viewTexture")
viewTgtAnchorShape = working.getIntegerProperty("viewTgtAnchorShape")
viewTgtAnchorSize = working.getSizeProperty("viewTgtAnchorSize")
timePoint = [
tp1_s, tp2_s, tp3_s, tp4_s, tp5_s, tp6_s, tp7_s, tp8_s, tp9_s, tp10_s,
tp11_s, tp12_s, tp13_s, tp14_s, tp15_s, tp16_s, tp17_s
]
'''
count=0
for i in working.getNodes():
count=count+1
if count >100:
working.delNode(i)
'''
pretraitement(working, Locus, Negative, Positive, viewColor, viewLabel,
viewLayout, viewSize)
applyModelForce(working, viewLayout)
distanceGraph = createDistanceGraph(working)
maxDepth = 3
partitionnement(distanceGraph, maxDepth)
heatmap = createHeatmap(working, distanceGraph, timePoint)
#heatmap = working.getSubGraph("heatmap")
colorHeatmap(heatmap)
# distanceGraph = working.getSubGraph("distanceGraph")
# heatmap = working.getSubGraph("heatmap")
construireGrille(distanceGraph, heatmap, maxDepth)