Python Tree.populate方法代碼示例

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
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

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
    def test(self):
        # Text faces

        I = TreeImage()
        I.mode = "rect"
        I.aligned_header.add_face(self.headerF, 0)
        I.aligned_header.add_face(self.headerF, 1)
        I.aligned_header.add_face(self.headerF, 2)
        I.aligned_header.add_face(self.headerF, 3)

        I.aligned_foot.add_face(self.footF, 0)
        I.aligned_foot.add_face(self.footF, 1)
        I.aligned_foot.add_face(self.footF, 2)
        I.aligned_foot.add_face(self.footF, 3) 
        I.draw_aligned_faces_as_grid = True
        t = Tree()
        t.dist = 0
        t.populate(10)

        style = NodeStyleDict()
        style["fgcolor"] = "#ff0000"
        style["size"] = 20
        style.add_fixed_face(self.fixedF, "branch-right", 0)
        t.img_style = style
        
        t.render("./test.svg", layout=mylayout, tree_style=I)
        t.show(mylayout, tree_style=I)
        t.show(mylayout2, tree_style=I)

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
def get_example_tree():

    # sample sequence and a list of example motif types     
    seq = "LHGRISQQVEQSRSQVQAIGEKVSLAQAKIEKIKGSKKAIKVFSSAKYPAPERLQEYGSIFTDAQDPGLQRRPRHRIQSKQRPLDERALQEKLKDFPVCVSTKPEPEDDAEEGLGGLPSNISSVSSLLLFNTTENLYKKYVFLDPLAGAVTKTHVMLGAETEEKLFDAPLSISKREQLEQQVPENYFYVPDLGQVPEIDVPSYLPDLPGIANDLMYIADLGPGIAPSAPGTIPELPTFHTEVAEPLKVGELGSGMGAGPGTPAHTPSSLDTPHFVFQTYKMGAPPLPPSTAAPVGQGARQDDSSSSASPSVQGAPREVVDPSGGWATLLESIRQAGGIGKAKLRSMKERKLEKQQQKEQEQVRATSQGGHLMSDLFNKLVMRRKGISGKGPGAGDGPGGAFARVSDSIPPLPPPQQPQAEDEDDWES"
    motifs = [
        # seq.start, seq.end, shape, width, height, fgcolor, bgcolor
        [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
        [110, 150, "o", None, 10, "blue", "pink", None],
        [155, 180, "()", None, 10, "blue", "rgradient:purple", None],
        [160, 170, "^", None, 14, "black", "yellow", None],
        [172, 180, "v", None, 12, "black", "rgradient:orange", None],
        [185, 190, "o", None, 12, "black", "brown", None],
        [198, 200, "<>", None, 15, "black", "rgradient:gold", None],
        [210, 240, "compactseq", 2, 10, None, None, None],
        [300, 320, "seq", 10, 10, None, None, None],
        [310, 345, "<>", None, 15, "black", "rgradient:black", None],
    ]
    # Create a random tree and add to each leaf a random set of motifs
    # from the original set
    t = Tree()
    t.populate(10)
    for l in t.iter_leaves():
        seq_motifs = [list(m) for m in motifs] #sample(motifs, randint(2, len(motifs))) 

        seqFace = SeqMotifFace(seq, seq_motifs, intermotif_format="line",
                               seqtail_format="compactseq", scale_factor=1)
        seqFace.margin_bottom = 4
        f = l.add_face(seqFace, 0, "aligned")

    return t, TreeStyle()

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
def get_example_tree():
    t = Tree()
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.mode = "r"
    ts.show_leaf_name = False
    t.populate(10)
    return t, ts

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
def get_example_tree():
        
    t = Tree()
    t.populate(8, reuse_names=False)

    ts = TreeStyle()
    ts.layout_fn = master_ly
    ts.title.add_face(faces.TextFace("Drawing your own Qt Faces", fsize=15), 0)
    return t, ts

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
def get_example_tree():
    t = Tree()
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.mode = "c"
    ts.show_leaf_name = True
    ts.min_leaf_separation = 15
    t.populate(100)
    return t, ts

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
def get_example_tree():
    t = Tree()
    t.populate(10)
    ts = TreeStyle()
    ts.rotation = 45
    ts.show_leaf_name = False
    ts.layout_fn = rotation_layout
    
    return t, ts

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
def get_example_tree():

    t = Tree()
    t.populate(8)

    # Node style handling is no longer limited to layout functions. You
    # can now create fixed node styles and use them many times, save them
    # or even add them to nodes before drawing (this allows to save and
    # reproduce an tree image design)

    # Set bold red branch to the root node
    style = NodeStyle()
    style["fgcolor"] = "#0f0f0f"
    style["size"] = 0
    style["vt_line_color"] = "#ff0000"
    style["hz_line_color"] = "#ff0000"
    style["vt_line_width"] = 8
    style["hz_line_width"] = 8
    style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
    style["hz_line_type"] = 0
    t.set_style(style)

    #Set dotted red lines to the first two branches
    style1 = NodeStyle()
    style1["fgcolor"] = "#0f0f0f"
    style1["size"] = 0
    style1["vt_line_color"] = "#ff0000"
    style1["hz_line_color"] = "#ff0000"
    style1["vt_line_width"] = 2
    style1["hz_line_width"] = 2
    style1["vt_line_type"] = 2 # 0 solid, 1 dashed, 2 dotted
    style1["hz_line_type"] = 2
    t.children[0].img_style = style1
    t.children[1].img_style = style1

    # Set dashed blue lines in all leaves
    style2 = NodeStyle()
    style2["fgcolor"] = "#000000"
    style2["shape"] = "circle"
    style2["vt_line_color"] = "#0000aa"
    style2["hz_line_color"] = "#0000aa"
    style2["vt_line_width"] = 2
    style2["hz_line_width"] = 2
    style2["vt_line_type"] = 1 # 0 solid, 1 dashed, 2 dotted
    style2["hz_line_type"] = 1
    for l in t.iter_leaves():
        l.img_style = style2

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

    return t, ts

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
def layout(node):
    if node.is_leaf():
        # Add node name to laef nodes
        N = AttrFace("name", fsize=14, fgcolor="black")
        faces.add_face_to_node(N, node, 0)

        t = Tree()
        t.populate(10)

        T = TreeFace(t, small_ts)
        # Let's make the sphere transparent 
        T.opacity = 0.8
        # And place as a float face over the tree
        faces.add_face_to_node(T, node, 1, position="aligned")

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
def get_example_tree():
    # Create a random tree and add to each leaf a random set of motifs
    # from the original set
    t = Tree()
    t.populate(10)
    # for l in t.iter_leaves():
    #     seq_motifs = [list(m) for m in motifs] #sample(motifs, randint(2, len(motifs))) 

    #     seqFace = SeqMotifFace(seq, seq_motifs, intermotif_format="line",
    #                            seqtail_format="compactseq", scale_factor=1)
    #     seqFace.margin_bottom = 4
    #     f = l.add_face(seqFace, 0, "aligned")

    ts = TreeStyle()
    ts.layout_fn = layout
    t.show(tree_style=ts)
    return t, ts

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
from ete_dev import Tree
# generates a random tree
t = Tree();
t.populate(15);
print t
#
#
#                    /-qogjl
#          /--------|
#         |          \-vxbgp
#         |
#         |          /-xyewk
#---------|         |
#         |         |                    /-opben
#         |         |                   |
#         |         |          /--------|                    /-xoryn
#          \--------|         |         |          /--------|
#                   |         |         |         |         |          /-wdima
#                   |         |          \--------|          \--------|
#                   |         |                   |                    \-qxovz
#                   |         |                   |
#                   |         |                    \-isngq
#                    \--------|
#                             |                    /-neqsc
#                             |                   |
#                             |                   |                              /-waxkv
#                             |          /--------|                    /--------|
#                             |         |         |          /--------|          \-djeoh
#                             |         |         |         |         |
#                             |         |          \--------|          \-exmsn
#                              \--------|                   |

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
import sys
from ete_dev import Tree, faces, TreeStyle, COLOR_SCHEMES

sys.path.insert(0, "./")
def layout(node):
    if node.is_leaf():
        F= faces.PieChartFace([10,10,10,10,10,10,10,10,10,4,6], colors=COLOR_SCHEMES["set3"], width=100, height=100)
        F.border.width = None
        F.opacity = 0.8
        faces.add_face_to_node(F,node, 0, position="branch-right")
        F.background.color = "indianred"
        x = faces.TextFace("hola")
        faces.add_face_to_node(x,node, 1, position="branch-right")
        x.background.color = "blue"
    else:
        F= faces.BarChartFace([40,20,70,100,30,40,50,40,70,12], min_value=0, colors=COLOR_SCHEMES["spectral"])
        faces.add_face_to_node(F,node, 0, position="branch-top")
        
t = Tree()
ts = TreeStyle()
ts.layout_fn = layout
ts.mode = "r"
ts.show_leaf_name = False

t.populate(10)
t.show(tree_style=ts)

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
    # Center text according to masterItem size
    tw = text.boundingRect().width()
    th = text.boundingRect().height()
    center = masterItem.boundingRect().center()
    text.setPos(center.x()-tw/2, center.y()-th/2)
    
    return masterItem

def master_ly(node):
    if node.is_leaf():
        # Create an ItemFAce. First argument must be the pointer to
        # the constructor function that returns a QGraphicsItem. It
        # will be used to draw the Face. Next arguments are arbitrary,
        # and they will be forwarded to the constructor Face function.
        F = faces.DynamicItemFace(ugly_name_face, 100, 50)
        faces.add_face_to_node(F, node, 0, position="aligned")
  

t = Tree()
t.populate(8, reuse_names=False)

ts = TreeStyle()
ts.layout_fn = master_ly
ts.title.add_face(faces.TextFace("Drawing your own Qt Faces", fsize=15), 0)


t.render("item_faces.png", h=400, tree_style=ts)
# The interactive features are only available using the GUI
t.show(tree_style=ts)

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
from ete_dev import Tree, faces, AttrFace, TreeStyle, NodeStyle

def layout(node):
    # If node is a leaf, add the nodes name and a its scientific name
    if node.is_leaf():
        faces.add_face_to_node(AttrFace("name"), node, column=0)

t = Tree()
t.populate(8)

# Node style handling is no longer limited to layout functions. You
# can now create fixed node styles and use them many times, save them
# or even add them to nodes before drawing (this allows to save and
# reproduce an tree image design)

# Set bold red branch to the root node
style = NodeStyle()
style["fgcolor"] = "#0f0f0f"
style["size"] = 0
style["vt_line_color"] = "#ff0000"
style["hz_line_color"] = "#ff0000"
style["vt_line_width"] = 8
style["hz_line_width"] = 8
style["vt_line_type"] = 0 # 0 solid, 1 dashed, 2 dotted
style["hz_line_type"] = 0
t.set_style(style)

#Set dotted red lines to the first two branches
style1 = NodeStyle()
style1["fgcolor"] = "#0f0f0f"
style1["size"] = 0

# 需要導入模塊: from ete_dev import Tree [as 別名]
# 或者: from ete_dev.Tree import populate [as 別名]
  #  n4.size = (10, 10)
    #n2.size = 10
    #n3.size = 10
    #n5.size = 10
    #n2.dist = 0.1
    #n2.size = 1
    #n3.size = 1
    #n2.dist = 0.5
    
#t.populate(100)#, random_branches=True)
#t.write(outfile="test.nw")
ts.layout_fn = layout2
t.show(tree_style=ts)
ts.scale = 1
sys.exit()
t.show(tree_style=ts)

for x in xrange(30):
    t = Tree()
    t.dist = 0
    t.populate(100, random_branches=True)
    t.render("/tmp/kk.png", tree_style=ts)
sys.exit()
ts.layout_fn = layout
t.show(tree_style=ts)
ts.mode = "r"
t.show(tree_style=ts)