Python TreeStyle.margin_top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 margin_top [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 margin_top [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 margin_top [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)