Python TreeStyle.rotation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 rotation [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 TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import rotation [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 ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import rotation [as 别名]
def draw_tree(tree_string):
    
    t = Tree(tree_string, format=8)
    
    def mylayout(node):
        #if node.name != 'L':
        file = 'tmp/%s.png' % node.name
        new_face = faces.ImgFace(file)
        new_face.rotable = True
        new_face.rotation = -90
        #new_face.margin_top = 50
        new_face.margin_left = 15
        faces.add_face_to_node(new_face, node, column=0 , position='branch-top')
        
    ts = TreeStyle()
    ts.rotation = 90
    ts.layout_fn = mylayout
    t.show(tree_style = ts)
    plt.clf()

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import rotation [as 别名]
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()
ts.branch_vertical_margin = 10
ts.show_leaf_name = True
ts.rotation = 90
ts.scale=100
t.render("tree_test100.png",tree_style=ts)

ts.scale=1000
t.render("tree_test1000.png",tree_style=ts)
## compare to

#t = Tree( '("[a,b]",c);' )
#t.show()

# []

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import rotation [as 别名]
root = Tree()
node_cur = root

'''#######################
 Tree Style Begin
'''
ts = TreeStyle()
ts.title.add_face(TextFace("Tree example", fsize=8), column=0)
ts.scale = 50
ts.mode = 'r'

# left or right
ts.orientation = 1

ts.rotation = 270
ts.show_leaf_name = False
ts.show_branch_length = True
#ts.show_branch_length = True
'''
 Tree Style End
#######################'''




'''#######################
 Node Style Begin
'''
ns_root = NodeStyle()
ns_root["size"] = 10

# 需要导入模块: from ete3 import TreeStyle [as 别名]
# 或者: from ete3.TreeStyle import rotation [as 别名]
def heatmap_view(tree, orthologous_groups, save_dir):
    """Generates a heatmap of regulation states in all species."""
    light_tree = copy.deepcopy(tree)  # Tree copy for the light heatmap
    # Heat map settings
    rect_face_fgcolor = 'black'
    locus_tag_len = max(len(gene.locus_tag) + 5
                        for ortho_grp in orthologous_groups
                        for gene in ortho_grp.genes)
    rect_face_width = locus_tag_len * 8
    light_rect_face_width = 20
    rect_face_height = 20
    rotation = 90

    # Sort orthologous groups by the number of regulated genes in each group
    orthologous_groups = filter_and_sort_orthologous_grps(orthologous_groups)

    # For each species and its gene in each orthologous group, draw a rectangle
    for node, light_node in zip(tree.get_leaves(), light_tree.get_leaves()):
        for i, orthologous_grp in enumerate(orthologous_groups, start=1):
            #get all orthologs in group
            matching_genes = [g for g in orthologous_grp.genes \
            if g.genome.strain_name == node.name]

            #if there is ortholog
            if len(matching_genes) > 0:
                # Get the first ortholog from the genome in the group
                #this is the one with higher probability of regulation.
                #so this probability will be displayed for the group
                gene = matching_genes[0]
                p_regulation = gene.operon.regulation_probability
                p_notregulation = 1.0 - p_regulation
                p_absence = 0
            # No ortholog from this genome
            else:
                gene = None
                p_regulation = 0
                p_notregulation = 0
                p_absence = 1

            # Color of the rectangle is based on probabilities
            rect_face_bgcolor = rgb2hex(
                p_notregulation, p_regulation, p_absence)
            rect_face_text = ('%s [%d]' % (gene.locus_tag, gene.operon.operon_id)
                              if gene else '')
            rect_face_label = {'text': rect_face_text,
                               'font': 'Courier',
                               'fontsize': 8,
                               'color': 'black'}
            # Create the rectangle
            rect_face = RectFace(rect_face_width, rect_face_height,
                                 rect_face_fgcolor, rect_face_bgcolor,
                                 label=rect_face_label)
            light_rect_face = RectFace(light_rect_face_width, rect_face_height,
                                       rect_face_fgcolor, rect_face_bgcolor,
                                       label='')
            rect_face.rotation = -rotation
            light_rect_face.rotation = -rotation
            # Add the rectangle to the corresponding column
            node.add_face(rect_face, column=i, position='aligned')
            light_node.add_face(light_rect_face, column=i, position='aligned')

    ts = TreeStyle()
    # Add orthologous group descriptions
    descriptions = ['-'.join([grp.description, str(grp.NOGs)]) for grp in orthologous_groups]
    max_description_len = max(map(len, descriptions))
    descriptions = [
        '[%d]' % i + description + ' '*(max_description_len-len(description))
        for i, description in enumerate(descriptions, start=1)]
    for i, description in enumerate(descriptions, start=1):
        text_face = TextFace(description, ftype='Courier')
        text_face.hz_align = 1
        text_face.vt_align = 1
        text_face.rotation = -rotation
        ts.aligned_header.add_face(text_face, column=i)

    # Rotate the generated heatmap.
    ts.margin_left = 10
    ts.margin_top = 20
    ts.rotation = rotation
    ts.show_scale = False
    # For some reason, it can't render to PDF in color
    tree.render(os.path.join(save_dir, 'heatmap.svg'), tree_style=ts)
    light_tree.render(os.path.join(save_dir, 'heatmap_light.svg'), tree_style=ts)