Python TreeStyle.show_branch_support方法代码示例

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [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 ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]
def balanceplot(balances, tree,
                layout=None,
                mode='c'):
    """ Plots balances on tree.

    Parameters
    ----------
    balances : np.array
        A vector of internal nodes and their associated real-valued balances.
        The order of the balances will be assumed to be in level order.
    tree : skbio.TreeNode
        A strictly bifurcating tree defining a hierarchical relationship
        between all of the features within `table`.
    layout : function, optional
        A layout for formatting the tree visualization. Must take a
        `ete.tree` as a parameter.
    mode : str
        Type of display to show the tree. ('c': circular, 'r': rectangular).

    Note
    ----
    The `tree` is assumed to strictly bifurcating and
    whose tips match `balances.

    See Also
    --------
    TreeNode.levelorder
    """
    # The names aren't preserved - let's pray that the topology is consistent.
    ete_tree = Tree(str(tree))
    # Some random features in all nodes
    i = 0
    for n in ete_tree.traverse():
        if not n.is_leaf():
            n.add_features(weight=balances[-i])
            i += 1

    # Create an empty TreeStyle
    ts = TreeStyle()

    # Set our custom layout function
    if layout is None:
        ts.layout_fn = default_layout
    else:
        ts.layout_fn = layout
    # Draw a tree
    ts.mode = mode

    # 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 ete_tree, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [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 TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]
def get_tree_style():
    ts = TreeStyle()
    # ts.mode = 'c'
    ts.margin_top = 10
    ts.margin_bottom = 10
    ts.margin_left = 10
    ts.margin_right = 10
    ts.show_leaf_name = False
    ts.show_branch_length = False
    ts.show_branch_support = False
    ts.show_scale = False
    title = TextFace("     Tax Assignment Tree", fsize=10)
    title.hz_align = 2
    title.vt_align = 2
    ts.title.add_face(TextFace(" "), column=0)
    ts.title.add_face(TextFace(" "), column=0)
    ts.title.add_face(title, column=0)
    return ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [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 ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]
def newick_to_linkage(filePath):
    """ converts newick tree to scipy linkage matrix """
    tree                   = ClusterTree(filePath)
    leaves                 = tree.get_leaf_names()
    ts                     = TreeStyle()
    ts.show_leaf_name      = True
    ts.show_branch_length  = True
    ts.show_branch_support = True

    idx_dict = {}
    idx = 0
    for leaf in leaves:
        idx_dict[leaf] = idx
        idx += 1

    idx_labels = [idx_dict.keys()[idx_dict.values().index(i)] for i in range(len(idx_dict))]

    dmat = np.zeros((len(leaves), len(leaves))) # FIXME need to understand

    for leaf1, leaf2 in combinations(leaves, 2):
        d = tree.get_distance(leaf1, leaf2)
        dmat[idx_dict[leaf1], idx_dict[leaf2]] = dmat[idx_dict[leaf2], idx_dict[leaf1]] = d

    schlink = sch.linkage(scipy.spatial.distance.squareform(dmat),method='average',metric='euclidean')

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]
def get_default_tree_style(color_dict):
    ts = TreeStyle()
    ts.mode = "c"
    # ts.layout_fn = layout
    ts.margin_top = 50
    ts.margin_bottom = 0
    ts.margin_left = 50
    ts.margin_right = 50
    ts.show_scale = False
    ts.show_leaf_name = False
    ts.show_branch_length = False
    ts.show_branch_support = False
    for p, c in color_dict.iteritems():
        ts.legend.add_face(TextFace("    ", fsize=30), column=0)
        ts.legend.add_face(CircleFace(10, c), column=1)
        ts.legend.add_face(TextFace("   %s" % p, fsize=30), column=2)
    legend_margin_line = 5
    while legend_margin_line:
        ts.legend.add_face(TextFace(" "), column=0)
        ts.legend.add_face(TextFace(" "), column=1)
        ts.legend.add_face(TextFace(" "), column=2)
        legend_margin_line -= 1
    ts.legend_position = 3
    return ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]

#.........这里部分代码省略.........
        pass

    def ly_block_alg(node):
        if node.is_leaf():
            if 'sequence' in node.features:
                seqFace = SeqMotifFace(node.sequence, [])
                # [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
                motifs = []
                last_lt = None
                for c, lt in enumerate(node.sequence):
                    if lt != '-':
                        if last_lt is None:
                            last_lt = c
                        if c+1 == len(node.sequence):
                            start, end = last_lt, c
                            motifs.append([start, end, "()", 0, 12, "slategrey", "slategrey", None])
                            last_lt = None
                    elif lt == '-':
                        if last_lt is not None:
                            start, end = last_lt, c-1
                            motifs.append([start, end, "()", 0, 12, "grey", "slategrey", None])
                            last_lt = None

                seqFace = SeqMotifFace(node.sequence, motifs,
                                       intermotif_format="line",
                                       seqtail_format="line", scale_factor=ALG_SCALE)
                add_face_to_node(seqFace, node, ALG_START_COL, aligned=True)


    TRACKED_CLADES = ["Eukaryota", "Viridiplantae",  "Fungi",
                      "Alveolata", "Metazoa", "Stramenopiles", "Rhodophyta",
                      "Amoebozoa", "Crypthophyta", "Bacteria",
                      "Alphaproteobacteria", "Betaproteobacteria", "Cyanobacteria",
                      "Gammaproteobacteria",]

    # ["Opisthokonta",  "Apicomplexa"]

    colors = random_color(num=len(TRACKED_CLADES), s=0.45)
    lin2color = dict([(ln, colors[i]) for i, ln in enumerate(TRACKED_CLADES)])

    NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444')

    LABEL_START_COL = 10
    ALG_START_COL = 40
    ts = TreeStyle()
    ts.draw_aligned_faces_as_table = False
    ts.draw_guiding_lines = False
    ts.show_leaf_name = False
    ts.show_branch_support = False
    ts.scale = 160

    ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels]

    MIXED_RES = set()
    MAX_SEQ_LEN = 0
    NPR_TREES = []
    for n in tree.traverse():
        if hasattr(n, "tree_seqtype"):
            MIXED_RES.add(n.tree_seqtype)
        if hasattr(n, "tree_type"):
            NPR_TREES.append(n.tree_type)
        seq = getattr(n, "sequence", "")
        MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN)

    if MAX_SEQ_LEN:
        ALG_SCALE = min(1, 1000./MAX_SEQ_LEN)
        ts.layout_fn.append(ly_block_alg)

    if len(NPR_TREES) > 1:
        rF = RectFace(4, 4, "steelblue", "steelblue")
        rF.margin_right = 10
        rF.margin_left = 10
        ts.legend.add_face(rF, 0)
        ts.legend.add_face(TextFace(" NPR node"), 1)
        ts.legend_position = 3

    if len(MIXED_RES) > 1:
        rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA")
        rF.margin_right = 10
        rF.margin_left = 10
        ts.legend.add_face(rF, 0)
        ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1)
        ts.legend_position = 3


    try:
        tree.set_species_naming_function(spname)
        annotate_tree_with_ncbi(tree)
        a = tree.search_nodes(species='Dictyostelium discoideum')[0]
        b = tree.search_nodes(species='Chondrus crispus')[0]
        #out = tree.get_common_ancestor([a, b])
        #out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up
        tree.set_outgroup(out)
        tree.swap_children()
    except Exception:
        pass

    tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150)
    tree.render(outfile+'.svg', tree_style=ts, w=170, units='mm', dpi=150)
    tree.render(outfile+'.pdf', tree_style=ts, w=170, units='mm', dpi=150)

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]
from ete3 import Tree,TreeStyle,NodeStyle
import os
for tree in [file for file in os.listdir('.') if file and file.endswith('_phyml_tree.txt')]:
    #print tree
    try:
        with open( tree, 'r') as f:  # FIXME boot_trees verus phyml_tree
            t = Tree(open(tree,'r').read())
            ts = TreeStyle()
            ns = NodeStyle()
            ns['size']=0
            ts.show_leaf_name = True
            ts.show_branch_length = False
            ts.show_branch_support = True
            for n in t.traverse():
                n.set_style(ns)
            #t.show(tree_style=ts)
            t.render( os.getcwd()+'/'+tree.replace('_phyml_tree.txt', '.png'),tree_style = ts)
    except:
        pass

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]
"""

from ete3 import Tree, TreeStyle, NodeStyle

with open('/Users/diyadas/cdips/Topic-Ontology/SimpleWikiTree_u.txt','r') as f:
    treestr = f.readlines()[0]    
    

t = Tree( treestr.rstrip(),format=8)

circular_style = TreeStyle()
circular_style.mode = "c" # draw tree in circular mode
circular_style.scale = 120
circular_style.show_leaf_name = True
circular_style.show_branch_length = True
circular_style.show_branch_support = True
t.render("mytree.png", tree_style=circular_style)


nstyle = NodeStyle()
nstyle["hz_line_width"] = 3
nstyle["vt_line_width"] = 3

# 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():
   n.set_style(nstyle)



ts = TreeStyle()

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]
def main(args):
	if args.alignment:
		t = PhyloTree(args.tree, alignment=args.alignment, alg_format='fasta')
	else:
		t = PhyloTree(args.tree)

	if args.highlight_new:
		runs = read_runs(args.highlight_new)

	t.set_outgroup('EM_079422')
	t.ladderize()

	ts = TreeStyle()
	ts.show_leaf_name = False
	ts.show_branch_support = False
	ts.layout_fn = layout

	thick_hz_line = NodeStyle()
	thick_hz_line["hz_line_width"] = 8
	t.set_style(thick_hz_line)
	#t.children[0].set_style(thick_hz_line)
	#t.children[1].set_style(thick_hz_line)

	thick_vt_line = NodeStyle()
	thick_vt_line["vt_line_width"] = 4
	t.set_style(thick_vt_line)

	# header
	if not args.hide_annotations:
		ts.aligned_header.add_face(MyTextFace('Sample identifier', fstyle='Bold', fsize=8, tight_text=False), column = 1)
		ts.aligned_header.add_face(MyTextFace('Prefecture', fstyle='Bold', fsize=8, tight_text=False), column = 2)
		ts.aligned_header.add_face(MyTextFace('Sous-prefecture', fstyle='Bold', fsize=8, tight_text=False), column = 3)
		ts.aligned_header.add_face(MyTextFace('Village', fstyle='Bold', fsize=8, tight_text=False), column = 4)
		ts.aligned_header.add_face(MyTextFace('Sample received', fstyle='Bold', fsize=8, tight_text=False), column = 5)

	if args.positions:
		positions = read_positions(args.positions)

		alg_header = RulerFace(positions,
                              col_width=11,
                              height=0, # set to 0 if dont want to use values
                              kind="stick",
                              hlines = [0],
                              hlines_col = ["white"], # trick to hide hz line
                              )

		ts.aligned_header.add_face(alg_header, 6)

	#legend
	if args.legend:
		legend = {}
		for s in samples.values():
			legend[s['prefec']] = s['prefec__colour']
		for p in sorted(legend.keys()):
			ts.legend.add_face(CircleFace(4, legend[p]), column=0)
			ts.legend.add_face(MyTextFace(p, fsize=6, tight_text=False), column=1)	
		ts.legend_position=1

	if args.circular:
		ts.mode = "c"
		ts.arc_start = -180 # 0 degrees = 3 o'clock
		ts.arc_span = 180

#	t.show(tree_style=ts)
	t.render(args.output, tree_style=ts, w=1024)

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]

#.........这里部分代码省略.........
        these could be strings or integers denoting which group a sample
        belongs to.  It must be the same length as the samples in `table`.
        The index must be the same on `table` and `grouping` but need not be
        in the same order.
    tree : skbio.TreeNode
        A strictly bifurcating tree defining a hierarchical relationship
        between all of the features within `table`
    significance_test : function, optional
        A statistical significance function to test for significance between
        classes.  This function must be able to accept at least two 1D
        array_like arguments of floats and returns a test statistic and a
        p-value, or a single statistic. By default ``scipy.stats.f_oneway``
        is used.
    layout : function, optional
        A layout for formatting the tree visualization. Must take a
        `ete.tree` as a parameter.
    mode : str
        Type of display to show the tree. ('c': circular, 'r': rectangular).

    Returns
    -------
    ete_tree : ete.Tree
        ETE tree converted from the `skbio.TreeNode` object
    ts : ete.TreeStyle
        ETE tree style used for formatting the visualized tree,
        with the test statistic plotted on each of the internal nodes.

    Note
    ----
    The `skbio.TreeNode` is assumed to strictly bifurcating and
    whose tips match `table`.  Also, it is assumed that none
    of the values in `table` are zero.  Replace with a pseudocount
    if necessary.

    See also
    --------
    skbio.TreeNode.bifurcate
    skbio.stats.composition.ilr
    skbio.stats.multiplicative_replacement
    scipy.stats.f_oneway
    """

    if np.any(table <= 0):
        raise ValueError('Cannot handle zeros or negative values in `table`. '
                         'Use pseudo counts or ``multiplicative_replacement``.'
                         )

    if significance_test is None:
        significance_test = scipy.stats.f_oneway

    sorted_features = [n.name for n in tree.tips()][::-1]
    if len(sorted_features) != len(table.columns):
        raise ValueError('The number of tips (%d) in the tree must be equal '
                         'to the number features in the table (%d).' %
                         (len(sorted_features), len(table.columns)))
    table = table.reindex(columns=sorted_features)

    mat, cats = check_table_grouping(table, grouping)

    basis, nodes = phylogenetic_basis(tree)
    ilr_coords = ilr(mat, basis=basis)

    ete_tree = Tree(str(tree))

    _cats = set(cats)
    i = 0
    for n in ete_tree.traverse():
        if not n.is_leaf():
            diffs = [ilr_coords[(cats == x).values, i] for x in _cats]

            stat = significance_test(*diffs)
            if len(stat) == 2:
                n.add_features(weight=-np.log(stat[1]))
            elif len(stat) == 1:
                n.add_features(weight=stat)
            else:
                raise ValueError(
                    "Too many arguments returned by %s" %
                    significance_test.__name__)
            i += 1

    # Create an empty TreeStyle
    ts = TreeStyle()

    # Set our custom layout function
    if layout is None:
        ts.layout_fn = default_layout
    else:
        ts.layout_fn = layout

    # Draw a tree
    ts.mode = mode

    # 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 ete_tree, ts

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]
    args, unknown = parser.parse_known_args()
    
    t = Tree(args.i)
    ts = TreeStyle()
    
    if args.colorleaf:
        
        with open(args.colorleaf,'rU') as file_map:
            for line in file_map:
                if line:
                    leaf_color = list(map(str.strip,line.split('\t')))
                    print leaf_color
                    for leaf in t.get_leaves_by_name(leaf_color[0]):
                        leaf.set_style(NodeStyle())
                        
                        if leaf.name == leaf_color[0]:
                            leaf.img_style["bgcolor"] = leaf_color[1]
                        
    ts.show_leaf_name = not args.noleaf
    ts.show_branch_length = not args.nolength
    ts.show_branch_support = not args.nosupport

    if args.circular:
        ts.mode = "c"
        
    ext="svg"
    if args.ext:
       ext = args.ext
       
    t.render(args.o+ext, w=183, tree_style=ts, units="mm")

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import show_branch_support [as 别名]
def run(args):
    if args.text_mode:
        from ete3 import Tree
        for tindex, tfile in enumerate(args.src_tree_iterator):
            #print tfile
            if args.raxml:
                nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
                t = Tree(nw)
            else:
                t = Tree(tfile)

            print(t.get_ascii(show_internal=args.show_internal_names,
                              attributes=args.show_attributes))
        return

    import random
    import re
    import colorsys
    from collections import defaultdict
    from ete3 import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle,
                         add_face_to_node, random_color)

    global FACES

    if args.face:
        FACES = parse_faces(args.face)
    else:
        FACES = []

    # VISUALIZATION
    ts = TreeStyle()
    ts.mode = args.mode
    ts.show_leaf_name = True
    ts.tree_width = args.tree_width


    for f in FACES:
        if f["value"] == "@name":
            ts.show_leaf_name = False
            break

    if args.as_ncbi:
        ts.show_leaf_name = False
        FACES.extend(parse_faces(
            ['value:@sci_name, size:10, fstyle:italic',
             'value:@taxid, color:grey, size:6, format:" - %s"',
             'value:@sci_name, color:steelblue, size:7, pos:b-top, nodetype:internal',
             'value:@rank, color:indianred, size:6, pos:b-bottom, nodetype:internal',
         ]))


    if args.alg:
        FACES.extend(parse_faces(
            ['value:@sequence, size:10, pos:aligned, ftype:%s' %args.alg_type]
         ))

    if args.heatmap:
        FACES.extend(parse_faces(
            ['value:@name, size:10, pos:aligned, ftype:heatmap']
         ))

    if args.bubbles:
        for bubble in args.bubbles:
            FACES.extend(parse_faces(
                ['value:@%s, pos:float, ftype:bubble, opacity:0.4' %bubble,
             ]))

    ts.branch_vertical_margin = args.branch_separation
    if args.show_support:
        ts.show_branch_support = True
    if args.show_branch_length:
        ts.show_branch_length = True
    if args.force_topology:
        ts.force_topology = True
    ts.layout_fn = lambda x: None

    for tindex, tfile in enumerate(args.src_tree_iterator):
        #print tfile
        if args.raxml:
            nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
            t = PhyloTree(nw)
        else:
            t = PhyloTree(tfile)


        if args.alg:
            t.link_to_alignment(args.alg, alg_format=args.alg_format)

        if args.heatmap:
            DEFAULT_COLOR_SATURATION = 0.3
            BASE_LIGHTNESS = 0.7
            def gradient_color(value, max_value, saturation=0.5, hue=0.1):
                def rgb2hex(rgb):
                    return '#%02x%02x%02x' % rgb
                def hls2hex(h, l, s):
                    return rgb2hex( tuple([int(x*255) for x in colorsys.hls_to_rgb(h, l, s)]))

                lightness = 1 - (value * BASE_LIGHTNESS) / max_value
                return hls2hex(hue, lightness, DEFAULT_COLOR_SATURATION)

#.........这里部分代码省略.........