Python TreeStyle.show_branch_length方法代码示例

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def get_example_tree():
    # Random tree
    t = Tree()
    t.populate(20, random_branches=True)

    # Some random features in all nodes
    for n in t.traverse():
        n.add_features(weight=random.randint(0, 50))

    # Create an empty TreeStyle
    ts = TreeStyle()

    # Set our custom layout function
    ts.layout_fn = layout

    # Draw a tree 
    ts.mode = "c"

    # We will add node names manually
    ts.show_leaf_name = False
    # Show branch data
    ts.show_branch_length = True
    ts.show_branch_support = True

    return t, ts

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def showTreeWithPictures(tree = None, alignment=None, branchLengths=True, bootstrapSupport=True, tolabel=None):

    print("ShowTreeWithPictures",tree, alignment, branchLengths,bootstrapSupport, tolabel)
    if alignment:
        t = EvolTree(tree, alignment,alg_format="paml")
        t.link_to_alignment(alignment,alg_format="paml")


    else:
        t = EvolTree(tree)

    nsFG = NodeStyle()
    nsFG["fgcolor"] = "darkgreen"
    nsFG["size"] = 8

    for node in t.traverse():
        print(node.node_id)
        if tolabel:
            if str(node.node_id) in tolabel:
                 node.set_style(nsFG)

    ts = TreeStyle()
    ts.show_leaf_name = True
    ts.show_branch_length = branchLengths
    ts.show_branch_support = bootstrapSupport
    out = FILE
    if branchLengths:
        out+="_Len"
    if bootstrapSupport:
        out+="_Boot"
    t.render(out+"_tree.pdf",tree_style=ts)
    t.render(out+"_tree.png",tree_style=ts)
    if INTERACTIVE:
        t.show(tree_style=ts)

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
 def plotTree(self, tree, out_fn=None, rotation=270, show_leaf_name=False, 
               show_branch_length=False, circularTree=False, show_division_nodes=True, 
               distance_between_branches=4, show_border=False, width=None, height=None):            
     from ete2 import TreeStyle        
     from PyQt4 import QtSvg, QtCore, QtGui
     from ete2.treeview import qt4_render, drawer, main
     
       
     ts = TreeStyle()   
     ts.show_scale = False
     ts.show_border = show_border
     ts.orientation = 1 # 0, tree is drawn from left-to-right. 1, tree is drawn from right-to-left
     ts.rotation = rotation
     ts.show_leaf_name = show_leaf_name
     ts.show_branch_length = show_branch_length
     if circularTree:
         ts.mode = 'c'
     else:
         ts.mode = 'r'
     ts.branch_vertical_margin = distance_between_branches
     
     
     def hideInternalNodesLayout(node):
         if not node.is_leaf():
             node.img_style["size"] = 0
     
     if show_division_nodes is False:
         ts.layout_fn = hideInternalNodesLayout
     
     if out_fn is not None:        
         scene  = qt4_render._TreeScene()
         img = ts
         
         tree_item, n2i, n2f = qt4_render.render(tree, img)
         scene.init_data(tree, img, n2i, n2f)
         tree_item.setParentItem(scene.master_item)
         scene.master_item.setPos(0,0)
         scene.addItem(scene.master_item)      
         main.save(scene, out_fn, w=width, h=height, dpi=600)    
           
     else:
         scene, img = drawer.init_scene(tree, None, ts)
         tree_item, n2i, n2f = qt4_render.render(tree, img)
         scene.init_data(tree, img, n2i, n2f)
     
         tree_item.setParentItem(scene.master_item)
         scene.addItem(scene.master_item)
     
         size = tree_item.rect()
         w, h = size.width(), size.height()
     
         svg = QtSvg.QSvgGenerator()
         svg.setFileName("test.svg")
         svg.setSize(QtCore.QSize(w, h))
         svg.setViewBox(size)
         pp = QtGui.QPainter()
         pp.begin(svg)            
         scene.render(pp, tree_item.rect(), tree_item.rect(), QtCore.Qt.KeepAspectRatio)

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def showTreeWithPictures(tree = None, alignment=None, branchLengths=True, bootstrapSupport=True, tolabel=None,showZScores=False,showLogs=False ):
    print(PICS)
    
    print("ShowTreeWithPictures",tree, alignment, branchLengths,bootstrapSupport, tolabel,showZScores,showLogs )
    if not alignment:
        nsFG = NodeStyle()
        nsFG["fgcolor"] = "darkgreen"
        nsFG["size"] = 8
        t = EvolTree(tree)
        #todo:label
        #
            
        for node in t.traverse():
            print(node.node_id)
            if tolabel:
                if str(node.node_id) in tolabel:
                     node.set_style(nsFG)
                #q'n'd 
            if (node.name.split("_")[0]+".png" in PICS):
                print(node.name.split("_")[0]+".png")
                node.add_face(ImgFace(PICDIR+os.sep+node.name.split("_")[0]+".png", height=50), column=1, position="aligned")
            #non GRZM identifier
            elif (node.name+".png" in PICS):
                print(node.name+".png")
                node.add_face(ImgFace(PICDIR+os.sep+node.name+".png", height=50), column=1, position="aligned")
            
            
        ts = TreeStyle()
        ts.show_leaf_name = True
        ts.show_branch_length = branchLengths
        ts.show_branch_support = bootstrapSupport
        out = FILE
        if branchLengths:
            out+="_Len"
        if bootstrapSupport:
            out+="_Boot"
        if Z:
            out+="_Z"
        if L:
            out+="_L"
        t.render(out+"_tree.pdf",tree_style=ts)
        t.render(out+"_tree.png",tree_style=ts)
        if INTERACTIVE:
            t.show(tree_style=ts)
        
    else:
        t = EvolTree(tree, alignment,alg_format="paml")
        t.link_to_alignment(alignment,alg_format="paml")
        #todo label
        #todo check treestyle
        
        #ts = TreeStyle()
        #ts.show_leaf_name = True
        #ts.show_branch_length = branchLength
        #ts.show_branch_support = bootstrapSupport
        t.show()

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def main(argv):

    print argv
    br = mechanize.Browser()
    directoryhtml = br.open(argv)
    t_soup = BeautifulSoup(directoryhtml.read())
    t_tables = t_soup.findAll('table',{"id":"people"})
    t_tbody = t_tables[0].findAll('tbody')
    t_trs = t_tbody[0].findAll('tr')
    for t_tr in t_trs:
        t_tds = t_tr.findAll('td')
        username = t_tds[0].find('a').find(text=True)
        email = t_tds[1].find('p').find(text=True)
        department = t_tds[2].find('p').find(text=True)
        title = t_tds[3].find('p').find(text=True)
        manager = t_tds[4].find('p').find(text=True)
        skypeid = t_tds[5].find('p').find(text=True)
        username_list.append(username)
        email_list.append(email[:email.find("@")])
        manager_list.append(manager)

    #Get the root manager
    rootname = getRootName()

    #Make the tree variable
    treeStr = getTree(rootname, "(", ")" + rootname + ";")
    treeStr = treeStr.replace("(,", "(")
    treeStr = treeStr.replace(",)", ")")
    treeStr = treeStr.replace(",,", ",")

    ts = TreeStyle()
    # Do not add leaf names automatically
    ts.show_leaf_name = False
    ts.show_branch_length = False
    ts.show_scale = False

    # Use my custom layout
    ts.layout_fn = my_layout

    t = Tree(treeStr, format=8)

    for n in t.traverse():
       nstyle = NodeStyle()
       nstyle["fgcolor"] = "red"
       nstyle["size"] = 15
       n.set_style(nstyle)

    count = 0
    addNodeCount(t, 0)
    #t.add_face(TextFace(str(addNodeCount(t, 0))), column=1, position = "branch-bottom")

    # Tell ETE to use your custom Tree Style
    t.show(tree_style=ts)
    t.render("tree_structure.png", w=183, units="mm")

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def load_tree(f_tree, f_align):
    # Tree style
    ts = TreeStyle()
    ts.show_leaf_name = True
    ts.show_branch_length = True
    ts.show_branch_support = True
    ts.branch_vertical_margin = 10    

    # Load phylogenetic tree
    tree = PhyloTree(f_tree.read())
    if f_align is not None:    
        tree.link_to_alignment(f_align.read())
    return tree, ts

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def get_tree_style(tree_file, abund, rownames):

    with open("matrix.txt", "w") as temp:
        cols = len(abund[0])
        header = "#Names"
        for i in xrange(cols):
            header += "\tOTU%d" % i
        temp.write("%s\n" % header)
        for i, row in enumerate(abund):
            temp.write("%s\t%s\n" % (rownames[i], '\t'.join([str(i) for i in row])))

    t = Tree(tree_file)
    t.convert_to_ultrametric(10)

    assert isinstance(abund, numpy.ndarray)
    assert isinstance(rownames, numpy.ndarray)
    ts = TreeStyle()
    ts.mode = "r"
    ts.show_leaf_name = False
    ts.show_scale = False
    ts.show_branch_length = False
    ts.branch_vertical_margin = 20
    ts.force_topology = True
    ts.optimal_scale_level = "full"
    ts.scale = 50
    ts.draw_guiding_lines = True
    ts.guiding_lines_type = 0
    ts.guiding_lines_color = "black"
    for n in t.traverse():
        if not n.is_leaf():
            nstyle = NodeStyle()
            n.set_style(nstyle)
            nstyle['size'] = 0
            nstyle['hz_line_width'] = 3
            nstyle['vt_line_width'] = 3
        else:
            nstyle = NodeStyle()
            n.set_style(nstyle)
            nstyle['size'] = 0
            nstyle['hz_line_width'] = 3
            nstyle['vt_line_width'] = 3
            nstyle['fgcolor'] = "Black"
            nstyle['shape'] = "square"
            name_face = AttrFace("name", fsize=14, ftype="Arial", fgcolor="black", penwidth=10, text_prefix=" ", text_suffix=" ")
            n.add_face(name_face, column=0, position="aligned")
            row_index = rownames.tolist().index(n.name)
            col = 1
            for i in xrange(10):
                col += 1
                n.add_face(CircleFace(5, color=get_color(abund, row_index, i)), column=col, position="aligned")
    return t, ts

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def get_tree_style(tree, metadata, colors):
    assert isinstance(tree, TreeNode)
    ts = TreeStyle()
    ts.mode = "c"
    ts.show_leaf_name = False
    ts.show_scale = False
    ts.show_branch_length = False
    ts.force_topology = True
    ts.optimal_scale_level = "mid"
    get_node_styles(tree, metadata, colors)

    for site, color in colors.items():
        if 'Gastro' in site:
            site = "GI"
        ts.legend.add_face(CircleFace(7, color), column=0)
        ts.legend.add_face(TextFace(" %s" % site, fsize=20), column=1)
    return ts

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def render_tree(tree, fname):
    # Generates tree snapshot 
    npr_nodestyle = NodeStyle()
    npr_nodestyle["fgcolor"] = "red"
    for n in tree.traverse():
        if hasattr(n, "nodeid"):
            n.set_style(npr_nodestyle)
    ts = TreeStyle()
    ts.show_leaf_name = True
    ts.show_branch_length = True
    ts.show_branch_support = True
    ts.mode = "r"
    iterface = faces.TextFace("iter")
    ts.legend.add_face(iterface, 0)

    tree.dist = 0
    tree.sort_descendants()
    tree.render(fname, tree_style=ts, w=700)

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def plot_tree(fixedTree,fileName):

    ## plot the tree
    def my_layout(node):
        if node.is_leaf():
            name_face = AttrFace("name",fsize=25)
            faces.add_face_to_node(name_face, node, column=0, position="branch-right")
        else:
            name_face = AttrFace("name", fsize=20, fgcolor="red")
            faces.add_face_to_node(name_face, node, column=0, position="branch-right")

    ts = TreeStyle()
    ts.show_leaf_name = False
    ts.show_branch_length = True
    ts.show_branch_support = True
    ts.scale =  180
    ts.layout_fn = my_layout
    out = fixedTree.render(fileName, units="mm",tree_style=ts,dpi=400)

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def main(argv):
	inputfile = ''
	outgroup = ''
	outputfile = ''

	ts = TreeStyle()
	ts.show_leaf_name = True
	ts.show_branch_length = False
	ts.show_branch_support = True

	ns = NodeStyle()
	ns["size"] = 0
	ns["vt_line_width"] = 2
	ns["hz_line_width"] = 2

	try:
		opts, args = getopt.getopt(argv,"hi:o:p:",["input=","outgroup=","-prefix-svg="])
	except getopt.GetoptError:
		print 'print-single-nwk.py -i <inputfile> -o <outgroup> -p <prefixsvg>'
		sys.exit(2)
	for opt, arg in opts:
		if opt == '-h':
			print 'print-single-nwk.py -i <inputfile> -o <outgroup> -p <prefixsvg>'
			sys.exit()
		elif opt in ("-i", "--input"):
			inputfile = arg
		elif opt in ("-o", "--outgroup"):
			outgroup = arg
		elif opt in ("-p", "--prefix-svg"):
			outputfile = arg
	# read tree
	t = Tree(inputfile)
	t.set_outgroup(outgroup)
	t.ladderize(1)

	for node in t.traverse():
		node.set_style(ns)

	# print final tree
	t.render(outputfile + ".svg", tree_style=ts)

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def showAlignmentWithTree(tree,alignment):
    print(tree)
    t = EvolTree(tree, alignment,alg_format="paml")
    nsFG = NodeStyle()
    nsFG["fgcolor"] = "darkgreen"
    nsFG["size"] = 15
    #print(t)
    #t.run_model ('fb.example')
    # t.show()

    t.link_to_alignment(alignment, alg_format="paml")
    for node in t.traverse():
        print(node)
        #if (node.name.split("_")[0] in GENES):
        #    print(node.name, node.node_id)
        #    if (node.name.split("_")[0] == "GRMZM2G083841"):
        #        node.add_face(ImgFace("83841.1.png", height=50, width=50), column=1, position="aligned")
        #    if (node.name.split("_")[0] == "GRMZM2G473001"):
        #        node.add_face(ImgFace("473001.png", height=50, width=50), column=1, position="aligned")
        node.add_face(TextFace(str(node.node_id)),column=0)
        #node.add_face(ImgFace("tux.png", height=50), column=1)
        #    node.set_style(nsFG)
        leaves  = node.get_leaf_names()
        #leaves = [l for l in leaves if l.split("_")[0] in GENES ]
        if leaves !=[]:
            print(node.name, node.node_id)
            #print(node.node_id)
    #t.mark_tree([8], marks=["#1"])
    #print(t.write())
    #print(alignment)
    #print(t)
    #t.show() #layout=evol_clean_layout)

    ts = TreeStyle()
    ts.show_leaf_name = True
    ts.show_branch_length = True
    ts.show_branch_support = True
    t = fakeUnroot(t)
    t.show(tree_style=ts)
    t.render("tree.pdf", tree_style=ts)

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
def setTreeStyle(style, layoutfunction):
    #consolidate options for showing trees
    #pass in string "circle" or "rect" and a layout function
    I = TreeStyle()
    if style == "circle":
        I.tree_width = 1200
        I.layout_fn = layoutfunction
        I.show_branch_length = False
        #I.show_branch_support = True
        I.show_leaf_name = False
        I.mode = "c"
        I.force_topology = True
        #I.legend_position = 3
        I.extra_branch_line_type = 1
        I.guiding_lines_type = 1
        I.guiding_lines_color = "#666666"
        I.extra_branch_line_color = "#666666"
        I.optimal_scale_level = "full"
        I.root_opening_factor = 0
        
    elif style =="rect":
        I = TreeStyle()
        I.layout_fn = layoutfunction
        I.show_leaf_name = False
        I.force_topology = True
        I.optimal_scale_level = "semi"
        
    else:
        I.layout_fn = layoutfunction
        I.show_leaf_name = False
        I.force_topology = True
        I.optimal_scale_level = "semi"
    return I

    

    

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]

#.........这里部分代码省略.........

        plt.tight_layout()  # fixes margins

        ## Conversion to Newick/ETE
        # Stuff we need
        from scipy.cluster.hierarchy import average, linkage, to_tree
        #from hcluster import linkage, to_tree
        from ete2 import Tree, TreeStyle, NodeStyle

        # Change it to a distance matrix
        T = to_tree(Z)

        # ete2 section
        root = Tree()
        root.dist = 0
        root.name = "root"
        item2node = {T: root}

        to_visit = [T]
        while to_visit:
            node = to_visit.pop()
            cl_dist = node.dist /2.0
            for ch_node in [node.left, node.right]:
                if ch_node:
                    ch = Tree()
                    ch.dist = cl_dist
                    ch.name = str(ch_node.id)
                    item2node[node].add_child(ch)
                    item2node[ch_node] = ch
                    to_visit.append(ch_node)

        # This is the ETE tree structure
        tree = root
        ts = TreeStyle()
        ts.show_leaf_name = True
        ts.show_branch_length = True
        ts.show_scale = False
        ts.scale =  None
        if orientation == "top":
            ts.rotation = 90
            ts.branch_vertical_margin = 10 # 10 pixels between adjacent branches

        # Draws nodes as small red spheres of diameter equal to 10 pixels
        nstyle = NodeStyle()
        nstyle["size"] = 0

        # Replace the node labels
        for leaf in tree:
            k = leaf.name
            k = int(k)
            leaf.name = labels[k]

        # Apply node styles to nodes
        for n in tree.traverse():
           n.set_style(nstyle)

        # Convert the ETE tree to Newick
        newick = tree.write()
        f = open('C:\\Users\\Scott\\Documents\\GitHub\\d3-dendro\\newickStr.txt', 'w')
        f.write(newick)
        f.close()

        # Save the image as .png...
        from os import path, makedirs

        # Using ETE
        folder = pathjoin(session_manager.session_folder(), constants.RESULTS_FOLDER)
        if (not os.path.isdir(folder)):
            makedirs(folder)

        # saves dendrogram as a .png with pyplot
        plt.savefig(path.join(folder, constants.DENDROGRAM_PNG_FILENAME))
        plt.close()
        # if orientation == "top":
        #     plt.figure(figsize=(20,80))
        # else:
        #     plt.figure(figsize=(80,20))

        pdfPageNumber, score, inconsistentMax, maxclustMax, distanceMax, distanceMin, monocritMax, monocritMin, threshold = utility.generateDendrogram(
            fileManager)
        session['dengenerated'] = True
        labels = fileManager.getActiveLabels()

        inconsistentOp = "0 " + leq + " t " + leq + " " + str(inconsistentMax)
        maxclustOp = "2 " + leq + " t " + leq + " " + str(maxclustMax)
        distanceOp = str(distanceMin) + " " + leq + " t " + leq + " " + str(distanceMax)
        monocritOp = str(monocritMin) + " " + leq + " t " + leq + " " + str(monocritMax)

        thresholdOps = {"inconsistent": inconsistentOp, "maxclust": maxclustOp, "distance": distanceOp,
                        "monocrit": monocritOp}

        managers.utility.saveFileManager(fileManager)
        session_manager.cacheAnalysisOption()
        session_manager.cacheHierarchyOption()
        import random
        ver = random.random() * 100
        return render_template('cluster.html', labels=labels, pdfPageNumber=pdfPageNumber, score=score,
                               inconsistentMax=inconsistentMax, maxclustMax=maxclustMax, distanceMax=distanceMax,
                               distanceMin=distanceMin, monocritMax=monocritMax, monocritMin=monocritMin,
                               threshold=threshold, thresholdOps=thresholdOps, ver=ver)

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import show_branch_length [as 别名]
#!/usr/bin/py
from ete2 import Tree
import sys
from ete2 import Tree, TreeStyle
from Bio import SeqIO
import os
import numpy as np

circular_style = TreeStyle()
circular_style.mode = "c" # draw tree in circular mode
circular_style.scale = 20
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = False
ts.show_branch_support = False
#need the Tree and sys packages
#script stole from https://www.biostars.org/p/97409/
def mean(array):
    return sum(array)/float(len(array))

def cache_distances(tree):
    ''' precalculate distances of all nodes to the root''' 
    node2rootdist = {tree:0}
    for node in tree.iter_descendants('preorder'):
        node2rootdist[node] = node.dist + node2rootdist[node.up]
    return node2rootdist

def collapse(tree, min_dist):
    # cache the tip content of each node to reduce the number of times the tree is traversed
    #Because the collapsing is happening from the inner nodes, we could iterate over the collapsing several times, but we will not.
    num_tips=len(tree.get_leaves())