Python Tree.render方法代码示例

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
    def ete_draw(self, fname=None):
        """ Draws the tree and saves it to a file.  If `fname` is None,
            show the tree instead of saving it.

            Args:
                fname: filename to save to (default=None)
        """
        if Cfg.USE_ETE3:
            def layout(node):
                faces.add_face_to_node(AttrFace("name"), node, column=0,
                                       position="branch-right")

            ts = TreeStyle()
            ts.show_leaf_name = False
            ts.layout_fn = layout
            ts.rotation = 90
            
            tree = EteTree(self.ete_str(), format=8)

            if fname:
                tree.render(fname, tree_style=ts)
            else:
                tree.show(tree_style=ts)
        else:
            # TODO maybe throw an error?
            pass

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
def show_tree(experiment_folder):
    model = MDPD.Hierachical_MDPD(1)
    model.load(os.path.join(experiment_folder, 'model.p'))

    width, depth = model.width, model.depth

    root = Tree()

    cache = [(0, root)]

    for i in range(depth + 1):
        foo = []

        for idx, node in cache:
            paren = int((idx - 1) / width)
            kid = idx - paren * width
            face = faces.ImgFace(os.path.join(experiment_folder, 'images', '{}_{}_{}.png'.format(idx, paren, kid)))
            node.add_face(face, 0)

            if i < depth:
                for k in range(width):
                    foo.append((idx * width + k + 1, node.add_child()))

        cache = foo

    ts = TreeStyle()
    ts.mode = "c"

    root.render(os.path.join(experiment_folder, 'images', 'tree_plot.png'), tree_style=ts)
    return root

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
def builtTree(phylo_tree_pic, paralogs_file):
    print("Aligning top 50 genes for phylogenetic tree...")
    # maken van alignment
    clustalw_cline = ClustalwCommandline("clustalw", infile=paralogs_file)
    stdout, stderr = clustalw_cline()
    # importeren van boom bestand
    tree = Tree(paralogs_file[:-6] + ".dnd")
    # bouwen en weggschrijven van boom
    tree.render(phylo_tree_pic)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
def drawTree(treeFile, ShowBool):
	"""
	Draw a tree from a phy file
	"""
	t = Tree(treeFile)
	imgFile = treeFile.replace(".tree", ".tree.png")

	# Basic tree style
	ts = TreeStyle()
	ts.show_leaf_name = True
	ts.show_branch_support = True
	ts.scale =  160

	# Draws nodes as small red spheres of diameter equal to 10 pixels
	nstyle = NodeStyle()
	nstyle["shape"] = "sphere"
	nstyle["size"] = 10
	nstyle["fgcolor"] = "darkred"
	#nstyle["faces_bgcolor"] = "pink"

	nstyle2 = NodeStyle()
	nstyle2["shape"] = "sphere"
	nstyle2["size"] = 10
	nstyle2["fgcolor"] = "darkblue"
	


	# Gray dashed branch lines
	nstyle["hz_line_type"] = 1
	nstyle["hz_line_color"] = "#cccccc"

	# Applies the same static style to all nodes in the tree. Note that,
	# if "nstyle" is modified, changes will affect to all nodes
	for n in t.traverse():
		if n.is_leaf():
			if n.name.split("|")[-1] == "GI":
				n.set_style(nstyle)
			if n.name.split("|")[-1] == "plasmid":
				n.set_style(nstyle2)
			gi = n.name.split("|")[1]
			n.name = n.name.split("|")[0] #+ "   " + n.name.split("|")[1]
			n.name = n.name.replace("_tRNA_modification_GTPase_", "")
			n.name = n.name.replace("_DNA", "")
			n.name = " " + n.name + " "
			if n.name[-1] == "_": n.name.rstrip()
			
			taxon, color = taxonToColour(gi)
			n.add_face(TextFace(taxon, fgcolor = color, fsize = 8), column=1, position="branch-right")
			#n.img_style["bgcolor"] = color
			
	if ShowBool == True: #permet de flipper les braches pour avoir des topologies similaires
		t.show(tree_style=ts)
	t.render(imgFile, w=393, units="mm", tree_style=ts)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
def plot_one_tree(newick_file, profile_dict, node_dict, params, prefix=''):
    t = Tree(newick_file, format=1)
    ts = get_tree_style()
    set_node_default(t, node_dict=node_dict)
    suf = ''
    if params['with_branch_circle']:
        add_node_circle(t, node_dict=node_dict)
        suf += '_circle'
    if params['with_leaf_pie'] and not params['with_branch_circle']:
        remove_node_circle(t, node_dict=node_dict)
    if params['with_leaf_pie']:
        add_pie_face(t, ts, profile_dict, group=params['group'])
        suf += '_pie'
    add_branch_text(t, tree_style=ts, node_dict=node_dict)
    set_node_style(t, node_dict=node_dict)

    if prefix:
        prefix += '_'
    pdf_file = '%s/%stax_tree%s.pdf' % (params['outdir'], prefix, suf)
    png_file = '%s/%stax_tree%s.png' % (params['outdir'], prefix, suf)
    t.render(pdf_file, tree_style=ts, dpi=100)
    image_trans(pdf_file, png_file)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
            nstyle['bgcolor'] = cp[0]
        elif abr == 'pbi':
            nstyle['bgcolor'] = cp[1]
        elif abr == 'pte':
            nstyle['bgcolor'] = cp[2]
        elif abr == 'ppe':
            nstyle['bgcolor'] = cp[3]
        elif abr == 'pse':
            nstyle['bgcolor'] = cp[4]
        elif abr == 'poc':
            nstyle['bgcolor'] = cp[5]
        elif abr == 'ptr':
            nstyle['bgcolor'] = cp[6]
        elif abr == 'pso':
            nstyle['bgcolor'] = cp[7]
        elif abr == 'pca':
            nstyle['bgcolor'] = cp[8]
        elif abr == 'tth':
            nstyle['bgcolor'] = cp[9]
        else:
            nstyle['bgcolor'] = "#000000"
        node.set_style(nstyle)


ts = TreeStyle()
#ts.show_leaf_name = False
ts.mode = 'c'
ts.title.add_face(TextFace(title, fsize=20), column=0)
#t.show(tree_style = ts)
t.render(outputfile, tree_style = ts)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
if __name__ == '__main__':
    params = read_params(sys.argv)
    mkdir(params['outdir'])
    modified_tax = '%s/tax_ass_modified.txt' % params['outdir']
    newick_file = '%s/tax_tree.nwk' % params['outdir']
    modify_tax_ass(params['tax_ass'], modified_tax)
    level_profile, total_profile = read_profile(modified_tax, params['profile'], params['top'])
    tree = read_tax(modified_tax, total_profile.T.mean())
    tree.adjust_profile()
    with open(newick_file, 'w') as out:
        out.write(str(tree))
    t = Tree(newick_file, format=1)
    ts = get_tree_style()

    set_node_default(t, node_dict=tree.nodes)
    suf = ''
    if params['with_branch_circle']:
        add_node_circle(t, node_dict=tree.nodes)
        suf += '_circle'
    if params['with_leaf_pie'] and not params['with_branch_circle']:
        remove_node_circle(t, node_dict=tree.nodes)
    if params['with_leaf_pie']:
        add_pie_face(t, ts, total_profile.T, group=params['group'])
        suf += '_pie'
    add_branch_text(t, tree_style=ts, node_dict=tree.nodes)
    set_node_style(t, node_dict=tree.nodes)

    pdf_file = '%s/tax_tree%s.pdf' % (params['outdir'], suf)
    t.render(pdf_file, tree_style=ts, dpi=100)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
        #print dendrogram
        #dendrogram.showFigure()

        print(tr.asciiArt())
        ts = TreeStyle()
        ts.show_leaf_name = True
        ts.show_branch_length = True
        ts.show_branch_support = True
        print('NEWICK='+json.dumps(newick))
        rooted_tree = Tree( newick )
        #svgfile = os.path.join('/Users/avoorhis/programming/jupyter/VAMPS_API',args.prefix+'_dendrogram.svg')
        svgfile = os.path.join(args.outdir,args.prefix+'_dendrogram.svg')
        print(os.getcwd())
        #print svgfile
        print('rendering0')
        rooted_tree.render(svgfile, tree_style=ts)  # writes file to tmp



    if args.function == 'pcoa_3d':
        #print('starting pcoa_3d')
        from skbio import DistanceMatrix
        dm = DistanceMatrix(dm1)
        #print(dm1)
        #print('end pcoa_3d')
        pcoa_data = pcoa(args, dm, datasets)
        
        #test_PCoA()

    if args.function == 'pcoa_2d':
        # if not args.metadata:

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
t.add_face(bottom_c0_r0, column=0, position="branch-bottom")
t.add_face(bottom_c0_r1, column=0, position="branch-bottom")

a = t&"a"
a.set_style(NodeStyle())
a.img_style["bgcolor"] = "lightgreen"

b = t&"b"
b.set_style(NodeStyle())
b.img_style["bgcolor"] = "indianred"

c = t&"c"
c.set_style(NodeStyle())
c.img_style["bgcolor"] = "lightblue"

t.set_style(NodeStyle())
t.img_style["bgcolor"] = "lavender"
t.img_style["size"] = 12

for leaf in t.iter_leaves():
    leaf.img_style["size"] = 12
    leaf.add_face(right_c0_r0, 0, "branch-right")
    leaf.add_face(aligned_c0_r1, 0, "aligned")
    leaf.add_face(aligned_c0_r0, 0, "aligned")
    leaf.add_face(aligned_c1_r1, 1, "aligned")
    leaf.add_face(aligned_c1_r0, 1, "aligned")

ts = TreeStyle()
ts.show_scale = False
t.render("face_positions.png", w=800, tree_style=ts)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
                try:
                    contig,start,stop = splitTblastn(unsanitized)
                    if contig in sanitizedToNot:
                        contig = sanitizedToNot[contig]
                    q = "SELECT organism FROM organisms INNER JOIN contigs ON contigs.organismid = organisms.organismid WHERE contigs.contig_mod=?;"
                    cur.execute(q, (contig,) )
                    for res in cur:
                        organism = res[0]
                except ValueError:
                    # Not a tblastn ID.
                    pass
            node.name = sanitizeString("%s_%s_%s" %(organism, annotation[0:63], unsanitized), False)
    
    t, ts = prettifyTree(t, title = gene + " cluster regions", show_bootstraps = False, ts=ts)

    if options.savepng:
        os.system("rm test.svg 2> /dev/null")
        t.render("%s.svg" %(options.outfile), tree_style=ts)
        os.system("convert -trim -depth 32 -background transparent %s.svg %s.png" %(options.outfile, options.outfile))

    if options.display:
        t.show(tree_style=ts)

    # Clean up
    con.close()
    try:
        sys.stderr.write("Deleting temporary directory %s...\n" %(tempdir))
        shutil.rmtree(tempdir)
    except OSError as exc:
        raise IOError("Unable to delete temporary directory %s" %(tempdir) )

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
class WebTreeHandler(object):
    def __init__(self, newick_str, tid, actions=None, style=None):
        self.tree = None
        self.nw_str = newick_str

        self.treeid = tid
        self.mapid = "map_" + tid
        self.imgid = "img_" + tid
        self.boxid = 'box_' + tid

        self.treeconfig_obj = None

    def init_nodeids(self):
        # Initialze node internal IDs
        for index, n in enumerate(self.tree.traverse('preorder')):
            n._nid = index

    def parse_newick(self):
        try:
           self.tree = Tree(self.nw_str)
        except NewickError:
           try:
              self.tree = Tree(self.nw_str, format=1)
           except NewickError as e:
              return "Newick Parsing Error: "+str(e)

        self.init_nodeids()
        return True

    def set_actions(self, actions=None):
        if actions is None:
           self.tree.actions = NodeActions()
        else:
           self.tree.actions = actions

    def set_style(self, style=None):
        if style is None:
           self.tree.tree_style = TreeStyle()
        else:
           self.tree.tree_style = style

    def set_tree_config(self, tcofg):
        self.treeconfig_obj = tcofg

    @timeit
    def redraw(self, top_offset=0,left_offset=0):
        #print "Inside redraw calling tree.render()"
        #os.environ["DISPLAY"]=":0" # Used by ete to render images
        base64_img, img_map = self.tree.render("%%return.PNG", tree_style=self.tree.tree_style)
        #print "Inside redraw calling get_html_map()...."
        html_map = self.get_html_map(img_map)

        ete_link = '<div style="margin:0px;padding:0px;text-align:left;"><a href="http://etetoolkit.org" style="font-size:7pt;" target="_blank" >Powered by etetoolkit</a></div>'
        html_img = """<img id="%s" class="ete_tree_img" USEMAP="#%s" onLoad="javascript:bind_popup(%s,%s);" src="data:image/gif;base64,%s">""" %(self.imgid, self.mapid, left_offset, top_offset, base64_img)

        tree_div_id = self.boxid
        #print "returning html from redraw method...."
        return html_map+ '<div id="%s" >'%tree_div_id + html_img + ete_link + "</div>"

    #------------------------------------------
    def save_image(self, img_format):
        img_url = os.path.join("http://phylo.cs.nmsu.edu:8080/TreeViewer/demo/tmp_dev/", self.treeid+"."+img_format)
        img_path = os.path.join("/var/www/html/TreeViewer/demo/tmp_dev/", self.treeid+"."+img_format)        
        img = self.tree.render(img_path, tree_style=self.tree.tree_style)
        #print "returning from save image"
        return '<a target="_blank" href="%s">Download Image</a>' %(img_url)
    #------------------------------------------
    def get_html_map(self, img_map):
        html_map = '<MAP NAME="%s" class="ete_tree_img">' %(self.mapid)
        #print "get_html_map method called......."
        if img_map["nodes"]:
            for x1, y1, x2, y2, nodeid, text in img_map["nodes"]:
                text = "" if not text else text
                area = img_map["node_areas"].get(int(nodeid), [0,0,0,0])
                html_map += """ <AREA SHAPE="rect" COORDS="%s,%s,%s,%s"
                                onMouseOut='unhighlight_node();'
                                onMouseOver='highlight_node("%s", "%s", "%s", %s, %s, %s, %s);'
                                onClick='show_actions("%s", "%s");'
                                href="javascript:void('%s');">""" %\
                    (int(x1), int(y1), int(x2), int(y2),
                     self.treeid, nodeid, text, area[0], area[1], area[2]-area[0], area[3]-area[1],
                     self.treeid, nodeid,
                     nodeid)

        if img_map["faces"]:
            for x1, y1, x2, y2, nodeid, text in img_map["faces"]:
                text = "" if not text else text
                area = img_map["node_areas"].get(int(nodeid), [0,0,0,0])
                html_map += """ <AREA SHAPE="rect" COORDS="%s,%s,%s,%s"
                                onMouseOut='unhighlight_node();'
                                onMouseOver='highlight_node("%s", "%s", "%s", %s, %s, %s, %s);'
                                onClick='show_actions("%s", "%s", "%s");'
                                href='javascript:void("%s");'>""" %\
                    (int(x1),int(y1),int(x2),int(y2),
                     self.treeid, nodeid, text, area[0], area[1], area[2]-area[0], area[3]-area[1],
                     self.treeid, nodeid, text,
                     text,
                     )
        html_map += '</MAP>'
        #print "returning html from get_html_map()...."
#.........这里部分代码省略.........

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
            print tg_names
            c_a = tree.get_common_ancestor(tg_names)
            #attempt to calculate distance on a version of the tree in which branches below some support threshold have been deleted
#            closest_leaves = []
 #           for leaf in closest_other_group:
  #              closest_leaves.append(leaf.name)
   #         target_leaves = []
    #        for leaf in target_group:
     #           target_leaves.append(leaf.name)
      #      collapsed_tree = tree
       #     for node in collapsed_tree:
        #        if node.support < 0.5:
         #           node.delete()
          #  target_ca = collapsed_tree.get_common_ancestor(target_leaves)
           # closest_ca = collapsed_tree.get_common_ancestor(closest_leaves)
         #   collapsed_distance = collapsed_tree.get_distance(target_ca, closest_ca, topology_only=True)
            print sys.argv[1] + "\tEuks not monophyletic\t" + str(len(eukaryote_seqs)) + "\t" + str(c_a.support) + "\t" + str(size_target_group) + "\t" + str(shortest_distance) + "\t" + str(num_sgs) 
        else:
            print sys.argv[1] + "\t" + answer[0]
#If euks are monophyletic, what is the max. number allowed for the gene to be considered a candidate LGT?
#euk sequence is part of a euk clade nested within bacteria, and the eukaryotes are not monophyletic in the tree [what about the case where the LGT is the only copy in euks?]
#tree.render(out_tree)
    except:
        raise
#uncomment the following to make a PDF of the tree
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_support = True
ts.show_branch_length = False
tree.render(out_tree, tree_style=ts)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
#!/usr/bin/python
from ete3 import Tree, NodeStyle
from pyies.userOptions import basePath
import os.path

spTree1F = os.path.join(basePath, 'analysis', 'iesdb', 'speciesTree1.nhx')
spTree2F = os.path.join(basePath, 'analysis', 'iesdb', 'speciesTree2.nhx')
spTree3F = os.path.join(basePath, 'analysis', 'iesdb', 'speciesTree3b.nhx')
outT1 = os.path.join(basePath, 'analysis', 'figures', 'spTree1.png')
outT2 = os.path.join(basePath, 'analysis', 'figures', 'spTree2.png')
outT3 = os.path.join(basePath, 'analysis', 'figures', 'spTree3.png')

for tF, oF in zip([spTree1F, spTree2F, spTree3F], [outT1, outT2, outT3]):
    t = Tree(tF)
    t.sort_descendants(attr='O')
    for node in t.traverse():
        nstyle = NodeStyle()
        nstyle["size"] = 0
        node.set_style(nstyle)
    #t.show()
    t.render(oF)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
			dst = t.get_distance(l)
			if dst != tree_dist:
				l.dist += tree_dist - dst
		sys.stdout.write('u')
	else:
		sys.stdout.write('\nERROR. Too many final species: will not force ultrametricity.\n')

#======================================================#
# EXPORT phylo
t.write(format=5, outfile=ophylo, dist_formatter='%0.20f')
## write the count of resultant species
f = open(ophylo, 'a')
f.write("\n"+str(nTrueSpecies)+"\n")
f.close()

if plot_trees:
	for leaf in t:
		leaf.name = leaf.sp
	t.render(ophylo+"_3PHYLO.png", w=183, units="mm")

#======================================================#
# FINAL PROMPTS
sys.stdout.write('P]\n') # Print
if not quiet: print "Runtime                  >> " + str(time.time() - init) + " sec"
if not quiet: print "Total species count      >> " + str(nTrueSpecies)
if nIndsSFS == nIndsORI:
	print "Exit status              >> OK!"
else: sys.exit("ERROR. A bug must be crawling around... Please, please, contact the programmer.")

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import render [as 别名]
from ete3 import Tree, TreeStyle, TextFace  # @UndefinedVariable

rand_newick = "((water, estuarine_open_water, inland_water)Water_bodies, artificial_surface, cloud, shadow, forest, grassland)Root;"
rand_tree = "rand_tree"
with open(rand_tree, 'w') as TREE:
    TREE.write(rand_newick)

# Reading tree t1 and t2
t1 = Tree(rand_newick, format=8)   # @UndefinedVariable

#t2 = Tree(rand_tree)         # @UndefinedVariable
ts = TreeStyle()
ts.show_leaf_name = True
ts.branch_vertical_margin = 20
ts.title.add_face(TextFace("Auckland LCDB", fsize=20), column=0)
ts.scale = 50
t1.add_face(TextFace("Root "), column=0, position = "branch-top")
for node in t1.traverse():
    if node.name == "Water_bodies":
        node.add_face(TextFace("Water_bodies"), column=0, position = "branch-top")

print(t1)
t1.render("mytree.png", tree_style=ts, dpi=300)