Python Graph.summary方法代码示例

# 需要导入模块: from igraph import Graph [as 别名]
# 或者: from igraph.Graph import summary [as 别名]
def plotTreeFromString(treeString, colordict, plotFile):
    """
    Plots a tree from the 'brackets tree' format
    :param treeString:
    :param colordict: defines the colors of the nodes by label (e.g. 1 to 5)
    :param plotFile: output file (.png)
    :return:
    """
    g = Graph()
    splitted = treeString.split("(")

    level = -1
    parents = dict()
    parentIds = dict()
    levelCount = dict()
    for part in splitted:
        if len(part)<1:
            continue
        else: #label follows
            level+=1
            count = levelCount.get(level,0)
            levelCount[level] = count+1
            #print "level %d" % level
            label = part[0]
            #print part.split()
            if len(part.split())>1: #leaf node
                label, wordPlusEnding = part.split()
                #print part, "at leaf"
                endings = wordPlusEnding.count(")")
                word = wordPlusEnding.strip(")")
                g.add_vertex(label=word, color=colordict[int(label)])
                #print "added node %d" % (len(g.vs)-1)
                currentNode = len(g.vs)-1
                p = parents[level-1]
                g.add_edge(currentNode,p)#add edge to parent
                #print "added edge %d-%d" % (len(g.vs)-1, parentIds[level-1])
                level-=endings
                #print "word", word
            else:
                g.add_vertex(label=label, color=colordict[int(label)])
                currentNode = g.vs[len(g.vs)-1]
                #print "added node %d" % (len(g.vs)-1)
                if level != 0:
                    p = parents[level-1]
                    g.add_edge(currentNode,p)#add edge to parent
                    #print "added edge %d-%d" % (len(g.vs)-1, parentIds[level-1])

                parent = currentNode
                parentId = len(g.vs)-1
                parents[level] = parent
                parentIds[level] = parentId
                print parentIds

        print g.summary()
        layout = g.layout_reingold_tilford(mode="in", root=0)
        plot(g, plotFile, layout=layout, bbox = (2000, 1000), margin = 100)

# 需要导入模块: from igraph import Graph [as 别名]
# 或者: from igraph.Graph import summary [as 别名]

#.........这里部分代码省略.........
		for p in self.plst:
			p.srlst = list(set(p.rlst))
			for r in p.srlst:
				#print r
				#print r.__dict__
				r.plst.append(p)
			for prim in p.primlst:
				for i in range(2):
					for c in prim[i]:
						if c not in p.sclst:
							p.sclst.append(c)
							c.cplst.append(p)
				
			

	def create_dgraph(self):
		""" initializes self.graph: the total directed graph of reactions. It ereases any preceding graph. """
		self.dgraph = Graph(0,directed = True)
		cnlst = []
		rnlst = []
		rlinks = []
		for rct in self.rlst:
			rnlst.append(rct.name)	
			for i in rct.innames:
				cnlst.append(i)
				rlinks.append((i,rct.name))
			for o in rct.outnames:
				cnlst.append(o)
				rlinks.append((rct.name,o))
			if rct.reversible == True:
				rnlst.append(rct.name+'_r')
				for o in rct.innames:
					rlinks.append((rct.name+'_r',o))
				for i in rct.outnames:
					rlinks.append((i,rct.name+'_r'))
		cnlst = list(set(cnlst))
		cinpathlst = [self.gsearch(cn).inpath if self.gsearch(cn) != None else [] for cn in cnlst]
		rnlst = list(set(rnlst))
		rinpathlst = [self.rsearch(rn).inpath if '_r' not in rn else self.rsearch(rn[0:len(rn)-2]) for rn in rnlst]
		cnlst.extend(rnlst)
		cinpathlst.extend(rinpathlst)
		self.dgraph.add_vertices(cnlst)
		self.dgraph.add_edges(rlinks)
		self.dgraph.vs['inpath'] = cinpathlst
		#print rlinks[len(rlinks)-3000:len(rlinks)-1]
		print self.dgraph.summary()

	
	def create_pgraphs(self,filterlst):
		""" create the graphs of all the pathways and initialize the corresponding variable """
		for p in self.plst:
			p.dependence(self)
		print '\nprimgraph'
		for p in self.plst:
			p.create_primgraph(filterlst)
		print '\ntotgraph\n'
		for p in self.plst:
			p.create_totgraph(filterlst)

	def create_filterlst(self,threshold):
		""" create a filtering list nlst containing all the vertex in dgraph that have a degree higher than threshold """

		lst = []
		nlst = []
		for v in range(self.dgraph.vcount()):
			if self.dgraph.degree(v) > threshold:
				lst.append(v)
				nlst.append(self.dgraph.vs['name'][v])
		print 'NUMBER OF ELEMENTS TO FILTER: '+str(len(lst))
		print nlst
		return nlst

	def stoichmat(self):
		""" outputs the full stoichiometric matrix of the system """

		smat = []
		clst = []
		rlst = []
		rev = []

		for r in self.rlst:
			if r.nobalance == False:
				if r.name not in rlst:
					rlst.append(r.name)
					rev.append(r.reversible)
				else:
					print 'error in STOICHMAT: reaction\t',r.name,'\talready present!'
			for cname in union(r.innames[:],r.outnames[:]):
				if cname not in clst:
					clst.append(cname)

		for r in self.rlst:
			if r.nobalance == False:
				#create the stoichiometric vector
				rclst = r.innames[:]
				rclst.extend(r.outnames[:])
				sv = [r.slst[[i for i,b in enumerate(rclst) if b == cname][0]] if cname in rclst else 0 for cname in clst]
				smat.append(sv)

		return [smat,clst,rlst,rev]