Python TreeStyle.layout_fn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 layout_fn [as 别名]
def get_example_tree():

    # Set dashed blue lines in all leaves
    nst1 = NodeStyle()
    nst1["bgcolor"] = "LightSteelBlue"
    nst2 = NodeStyle()
    nst2["bgcolor"] = "Moccasin"
    nst3 = NodeStyle()
    nst3["bgcolor"] = "DarkSeaGreen"
    nst4 = NodeStyle()
    nst4["bgcolor"] = "Khaki"


    t = Tree("((((a1,a2),a3), ((b1,b2),(b3,b4))), ((c1,c2),c3));")
    for n in t.traverse():
        n.dist = 0
    
    n1 = t.get_common_ancestor("a1", "a2", "a3")
    n1.set_style(nst1)
    n2 = t.get_common_ancestor("b1", "b2", "b3", "b4")
    n2.set_style(nst2)
    n3 = t.get_common_ancestor("c1", "c2", "c3")
    n3.set_style(nst3)
    n4 = t.get_common_ancestor("b3", "b4")
    n4.set_style(nst4)
    ts = TreeStyle()
    ts.layout_fn = layout
    ts.show_leaf_name = False

    ts.mode = "c"
    ts.root_opening_factor = 1
    return t, ts

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import layout_fn [as 别名]
def build_vis():
	ts = TreeStyle()
	ts.mode = "c"
	ts.arc_start = 0 # 0 degrees = 3 o'clock
	ts.arc_span = 360
	ts.layout_fn = my_layout # Use custom layout
	return ts

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import layout_fn [as 别名]
 def generateImage(self, tree):
     ts = TreeStyle()
     ts.layout_fn = self.__layout__
     ts.mode = "c"
     ts.show_leaf_name = False
     tree.render(self.treePNGFile, w=1000, tree_style = ts)
     tree.render(self.treeSVGFile, w=250, tree_style = ts)

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import layout_fn [as 别名]
def visualizeTree(sTreePath, pathToSfamilies, bootValue, width, height):
    # Random tree
    stree = Tree()
    stree = readTreeFromFile(sTreePath)
   
    snodesStatDic={}
    snodesStatDic= getFamiliesStatisticsForEachNode(pathToSfamilies, bootValue)
    #print snodesStatDic
    # Some random features in all nodes
    for n in stree.traverse():
        if n.name in snodesStatDic.keys():
            total= reduce(lambda x,y: x+y, snodesStatDic[n.name])
            #norm= [(x*100)/total for x in snodesStatDic[n.name]]
            norm= [x for x in snodesStatDic[n.name]]
            n.add_features(pie_data=norm)
    # Create an empty TreeStyle
    ts = TreeStyle()

    # Set our custom layout function
    ts.layout_fn=layout

    # Draw a tree 
    ts.mode = "r"
    
    #ts.force_topology= False
    ts.complete_branch_lines_when_necessary= True
    # 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 stree, ts

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import layout_fn [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 layout_fn [as 别名]
def render_tree(sk_tree, tip_hues, tip_lums, saturation=0.9, output_fp=None, supress_display=False):
    ete_tree = Tree(str(sk_tree))
    tree_tips = [x.name for x in sk_tree.tips()]

    for ete_leaf in ete_tree.iter_leaves():
        if (ete_leaf.name not in tree_tips) and (ete_leaf.name[1:-1] in tree_tips):
            ete_leaf.name = ete_leaf.name[1:-1]
        elif ete_leaf.name not in tree_tips:
            print 'leaf {0} in ete-parsed tree not found in skbio tree {1}'.format(ete_leaf.name,str(sk_tree.ascii_art()))
            raise KeyError

    for n in ete_tree.traverse():
        if n.is_leaf():
            hex_color = hls_to_rgb_hex(tip_hues[n.name], tip_lums[n.name], saturation)
            n.add_features(tip_color=hex_color)

    style = NodeStyle()
    style["size"] = 0
    for l in ete_tree.traverse():
        l.set_style(style)

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

    if output_fp:
        ete_tree.render(output_fp, tree_style = ts)

    if not supress_display:
        ete_tree.show(tree_style = ts)

    return

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

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

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

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

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import layout_fn [as 别名]
def taxo_msa(outfile='taxo_msa.svg',taxids=[],annotation='',msa=[],title='',width=2000):
    """
    Visualize MSA together with a taxonomy tree
    taxids - list of taxids in the same order as seqs in msa
    """
    # taxid2gi={f_df.loc[f_df.gi==int(gi),'taxid'].values[0]:gi for gi in list(f_df['gi'])}
    # gi2variant={gi:f_df.loc[f_df.gi==int(gi),'hist_var'].values[0] for gi in list(f_df['gi'])}

    # msa_dict={i.id:i.seq for i in msa_tr}
    ncbi = NCBITaxa()
    taxids=map(int,taxids)

    t = ncbi.get_topology(taxids,intermediate_nodes=False)
    a=t.add_child(name='annotation')
    a.add_feature('sci_name','annotation')
    t.sort_descendants(attr='sci_name')
    ts = TreeStyle()
    def layout(node):
        # print node.rank
        # print node.sci_name
        if getattr(node, "rank", None):
            if(node.rank in ['order','class','phylum','kingdom']):   
                rank_face = AttrFace("sci_name", fsize=7, fgcolor="indianred")
                node.add_face(rank_face, column=0, position="branch-top")
        if node.is_leaf():
            sciname_face = AttrFace("sci_name", fsize=9, fgcolor="steelblue")
            node.add_face(sciname_face, column=0, position="branch-right")
        if node.is_leaf() and not node.name=='annotation':
            s=str(msa[taxids.index(int(node.name))].seq)
            seqFace = SeqMotifFace(s,[[0,len(s), "seq", 10, 10, None, None, None]],scale_factor=1)
            add_face_to_node(seqFace, node, 0, position="aligned")
            # gi=taxid2gi[int(node.name)]
            add_face_to_node(TextFace(' '+msa[taxids.index(int(node.name))].id),node,column=1, position = "aligned")
            # add_face_to_node(TextFace('      '+str(int(node.name))+' '),node,column=2, position = "aligned")
            # add_face_to_node(TextFace('      '+str(gi2variant[gi])+' '),node,column=3, position = "aligned")

        if node.is_leaf() and node.name=='annotation':
            if(annotation):
                s=annotation
                # get_hist_ss_in_aln_as_string(msa_tr)
            else:
                s=' '*len(msa[0].seq)
            seqFace = SeqMotifFace(s,[[0,len(s), "seq", 10, 10, None, None, None]],scale_factor=1)
            add_face_to_node(seqFace, node, 0, position="aligned")
            add_face_to_node(TextFace(' '+'SEQ_ID'),node,column=1, position = "aligned")
            # add_face_to_node(TextFace('       '+'NCBI_TAXID'+' '),node,column=2, position = "aligned")
            # add_face_to_node(TextFace('       '+'Variant'+'       '),node,column=3, position = "aligned")



    ts.layout_fn = layout
    ts.show_leaf_name = False
    ts.title.add_face(TextFace(title, fsize=20), column=0)
    t.render(outfile, w=width, dpi=300, tree_style=ts)

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

# 需要导入模块: from ete2 import TreeStyle [as 别名]
# 或者: from ete2.TreeStyle import layout_fn [as 别名]
def drawTree(nwfile, outfile):
    from ete2 import Tree, TreeStyle, TextFace
    ts = TreeStyle()
    ts.show_leaf_name = False
    ts.layout_fn = my_layout
    ts.branch_vertical_margin = 12.75
    ts.orientation = 1
    titleFace = TextFace("Phylogenetic Tree", fsize=18, fgcolor="white")
    titleFace.margin_top = 15
    ts.title.add_face(titleFace, column=1)

    t = Tree(nwfile)
    t.render(outfile, tree_style=ts)