Python TreeStyle.tree_width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 tree_width [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 tree_width [as 别名]
def run(args):
    if args.text_mode:
        from ete2 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 ete2 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(map(lambda x: int(x*255), 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.........

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import tree_width [as 别名]
    SHAPE = 'c'
elif not args["-root"]:
    SHAPE = 'c'
else: SHAPE = args["-shape"]

tree_files = glob.glob( "{0}/trees/raxmltrees/*.nwk".format(INPUT_DIR))
small = [Tree( open(x).read() ) for x in tree_files]
for x in small:
    x.set_outgroup(ROOT)
    x.ladderize()
names = [x[1+x.rindex("/"):x.rindex(".")] for x in tree_files]
big = Tree( open("{0}/clusters/cluster_dendrogram.nwk".format(INPUT_DIR)).read() )
print names
small_d = dict(zip(names,small))
small_ts = TreeStyle()
small_ts.tree_width = 100
small_ts.show_leaf_name = True

big_ts = TreeStyle()
big_ts.show_leaf_name = False
big_ts.layout_fn = layout
if SHAPE == 'v':    
    big_ts.rotation = 90
    small_ts.rotation = -90
    big_ts.mode = 'r'
else: big_ts.mode = SHAPE


# big.show(tree_style=big_ts)
big.render("./treeoftrees.pdf",tree_style=big_ts)