def get_tree_style(self):
     ts = TreeStyle()
     ts.layout_fn = self.custom_layout
     ts.show_leaf_name = False
     ts.draw_guiding_lines = True
     ts.guiding_lines_type = 0
     ts.guiding_lines_color = "#000000"
     self._treestyle = ts
     return ts
 def run_action_change_style(self, tree, a_data):
     #print "action change style called.."        
     if tree.tree_style == self._treestyle:
        ts2 = TreeStyle()
        ts2.layout_fn = self.custom_layout
        ts2.show_leaf_name = False
        ts2.draw_guiding_lines = True
        ts2.guiding_lines_type = 0 #solid line
        ts2.guiding_lines_color = a_data
        tree.tree_style = ts2
        self._treestyle = ts2
     else:
        tree.tree_style = self._treestyle
Example #3
0
                    default="pies.svg")

args = parser.parse_args()
plot_tree, subtrees_dict, subtrees_topids = get_phyparts_nodes(
    args.species_tree, args.phyparts_root)

concord_dict, conflict_dict = get_concord_and_conflict(args.phyparts_root,
                                                       subtrees_dict,
                                                       subtrees_topids)
phyparts_dist, phyparts_pies = get_pie_chart_data(args.phyparts_root,
                                                  args.num_genes, concord_dict,
                                                  conflict_dict)

#Plot Pie Chart
ts = TreeStyle()
ts.show_leaf_name = False

ts.layout_fn = phyparts_pie_layout
nstyle = NodeStyle()
nstyle["size"] = 0
for n in plot_tree.traverse():
    n.set_style(nstyle)
    n.img_style["vt_line_width"] = 0

ts.draw_guiding_lines = True
ts.guiding_lines_color = "black"
ts.guiding_lines_type = 0
ts.scale = 30
ts.branch_vertical_margin = 10
plot_tree.convert_to_ultrametric()
my_svg = plot_tree.render(args.svg_name, tree_style=ts, w=595)
Example #4
0
def plot_tree_barplot(tree_file,
                      taxon2value_list_barplot,
                      header_list,
                      taxon2set2value_heatmap=False,
                      header_list2=False,
                      column_scale=True,
                      general_max=False,
                      barplot2percentage=False,
                      taxon2mlst=False):
    '''

    display one or more barplot

    :param tree_file:
    :param taxon2value_list:
    :param exclude_outgroup:
    :param bw_scale:
    :param barplot2percentage: list of bool to indicates if the number are percentages and the range should be set to 0-100

    :return:
    '''

    import matplotlib.cm as cm
    from matplotlib.colors import rgb2hex
    import matplotlib as mpl

    if taxon2mlst:
        mlst_list = list(set(taxon2mlst.values()))
        mlst2color = dict(zip(mlst_list, get_spaced_colors(len(mlst_list))))
        mlst2color['-'] = 'white'

    if isinstance(tree_file, Tree):
        t1 = tree_file
    else:
        t1 = Tree(tree_file)

    # Calculate the midpoint node
    R = t1.get_midpoint_outgroup()
    # and set it as tree outgroup
    t1.set_outgroup(R)

    tss = TreeStyle()
    value = 1
    tss.draw_guiding_lines = True
    tss.guiding_lines_color = "gray"
    tss.show_leaf_name = False

    if column_scale and header_list2:
        import matplotlib.cm as cm
        from matplotlib.colors import rgb2hex
        import matplotlib as mpl
        column2scale = {}
        for column in header_list2:
            values = taxon2set2value_heatmap[column].values()

            norm = mpl.colors.Normalize(vmin=min(values), vmax=max(values))
            cmap = cm.OrRd
            m = cm.ScalarMappable(norm=norm, cmap=cmap)
            column2scale[column] = m

    cmap = cm.YlGnBu  #YlOrRd#OrRd

    values_lists = taxon2value_list_barplot.values()

    scale_list = []
    max_value_list = []

    for n, header in enumerate(header_list):
        #print 'scale', n, header
        data = [float(i[n]) for i in values_lists]

        if barplot2percentage is False:
            max_value = max(data)  #3424182#
            min_value = min(data)  #48.23
        else:
            if barplot2percentage[n] is True:
                max_value = 100
                min_value = 0
            else:
                max_value = max(data)  #3424182#
                min_value = min(data)  #48.23
        norm = mpl.colors.Normalize(vmin=min_value, vmax=max_value)
        m1 = cm.ScalarMappable(norm=norm, cmap=cmap)
        scale_list.append(m1)
        if not general_max:
            max_value_list.append(float(max_value))
        else:
            max_value_list.append(general_max)

    for i, lf in enumerate(t1.iter_leaves()):

        #if taxon2description[lf.name] == 'Pirellula staleyi DSM 6068':
        #    lf.name = 'Pirellula staleyi DSM 6068'
        #    continue
        if i == 0:

            col_add = 0

            if taxon2mlst:
                header_list = ['MLST'] + header_list

            for col, header in enumerate(header_list):

                #lf.add_face(n, column, position="aligned")
                n = TextFace(' ')
                n.margin_top = 1
                n.margin_right = 2
                n.margin_left = 2
                n.margin_bottom = 1
                n.rotation = 90
                n.inner_background.color = "white"
                n.opacity = 1.
                n.hz_align = 2
                n.vt_align = 2

                tss.aligned_header.add_face(n, col_add + 1)

                n = TextFace('%s' % header)
                n.margin_top = 1
                n.margin_right = 2
                n.margin_left = 2
                n.margin_bottom = 2
                n.rotation = 270
                n.inner_background.color = "white"
                n.opacity = 1.
                n.hz_align = 2
                n.vt_align = 1
                tss.aligned_header.add_face(n, col_add)
                col_add += 2

            if header_list2:
                for col, header in enumerate(header_list2):
                    n = TextFace('%s' % header)
                    n.margin_top = 1
                    n.margin_right = 20
                    n.margin_left = 2
                    n.margin_bottom = 1
                    n.rotation = 270
                    n.hz_align = 2
                    n.vt_align = 2
                    n.inner_background.color = "white"
                    n.opacity = 1.
                    tss.aligned_header.add_face(n, col + col_add)

        if taxon2mlst:

            try:
                #if lf.name in leaf2mlst or int(lf.name) in leaf2mlst:
                n = TextFace(' %s ' % taxon2mlst[int(lf.name)])
                n.inner_background.color = 'white'
                m = TextFace('  ')
                m.inner_background.color = mlst2color[taxon2mlst[int(lf.name)]]
            except:
                n = TextFace(' na ')
                n.inner_background.color = "grey"
                m = TextFace('    ')
                m.inner_background.color = "white"

            n.opacity = 1.
            n.margin_top = 2
            n.margin_right = 2
            n.margin_left = 0
            n.margin_bottom = 2

            m.margin_top = 2
            m.margin_right = 0
            m.margin_left = 2
            m.margin_bottom = 2

            lf.add_face(m, 0, position="aligned")
            lf.add_face(n, 1, position="aligned")
            col_add = 2
        else:
            col_add = 0

        try:
            val_list = taxon2value_list_barplot[lf.name]
        except:
            if not taxon2mlst:
                val_list = ['na'] * len(header_list)
            else:
                val_list = ['na'] * (len(header_list) - 1)

        for col, value in enumerate(val_list):

            # show value itself
            try:
                n = TextFace('  %s  ' % str(value))
            except:
                n = TextFace('  %s  ' % str(value))
            n.margin_top = 1
            n.margin_right = 5
            n.margin_left = 10
            n.margin_bottom = 1
            n.inner_background.color = "white"
            n.opacity = 1.

            lf.add_face(n, col_add, position="aligned")
            # show bar
            try:
                color = rgb2hex(scale_list[col].to_rgba(float(value)))
            except:
                color = 'white'
            try:
                percentage = (value / max_value_list[col]) * 100
                #percentage = value
            except:
                percentage = 0
            try:
                maximum_bar = (
                    (max_value_list[col] - value) / max_value_list[col]) * 100
            except:
                maximum_bar = 0
            #maximum_bar = 100-percentage
            b = StackedBarFace([percentage, maximum_bar],
                               width=100,
                               height=10,
                               colors=[color, "white"])
            b.rotation = 0
            b.inner_border.color = "grey"
            b.inner_border.width = 0
            b.margin_right = 15
            b.margin_left = 0
            lf.add_face(b, col_add + 1, position="aligned")
            col_add += 2

        if taxon2set2value_heatmap:
            shift = col + col_add + 1

            i = 0
            for col, col_name in enumerate(header_list2):
                try:
                    value = taxon2set2value_heatmap[col_name][lf.name]
                except:
                    try:
                        value = taxon2set2value_heatmap[col_name][int(lf.name)]
                    except:
                        value = 0

                if int(value) > 0:
                    if int(value) > 9:
                        n = TextFace(' %i ' % int(value))
                    else:
                        n = TextFace(' %i   ' % int(value))
                    n.margin_top = 1
                    n.margin_right = 1
                    n.margin_left = 20
                    n.margin_bottom = 1
                    n.fgcolor = "white"
                    n.inner_background.color = rgb2hex(
                        column2scale[col_name].to_rgba(
                            float(value)))  #"orange"
                    n.opacity = 1.
                    lf.add_face(n, col + col_add, position="aligned")
                    i += 1
                else:
                    n = TextFace('  ')  #% str(value))
                    n.margin_top = 1
                    n.margin_right = 1
                    n.margin_left = 20
                    n.margin_bottom = 1
                    n.inner_background.color = "white"
                    n.opacity = 1.

                    lf.add_face(n, col + col_add, position="aligned")

        n = TextFace(lf.name, fgcolor="black", fsize=12, fstyle='italic')
        lf.add_face(n, 0)

    for n in t1.traverse():
        nstyle = NodeStyle()
        if n.support < 1:
            nstyle["fgcolor"] = "black"
            nstyle["size"] = 6
            n.set_style(nstyle)
        else:
            nstyle["fgcolor"] = "red"
            nstyle["size"] = 0
            n.set_style(nstyle)

    return t1, tss
def bub_tree(tree, fasta, outfile1, root, types, c_dict, show, size, colours,
             field1, field2, scale, multiplier, dna):
    """
    :param tree: tree object from ete
    :param fasta: the fasta file used to make the tree
    :param outfile1: outfile suffix
    :param root: sequence name to use as root
    :param types: tree type: circular (c) or rectangle (r)
    :param c_dict: dictionary mapping colour to time point (from col_map)
    :param show: show the tree in a gui (y/n)
    :param size: scale the terminal nodes by frequency information (y/n)
    :param colours: if using a matched fasta file, colour the sequence by charge/IUPAC
    :param field1: the field that contains the size/frequency value
    :param field2: the field that contains the size/frequency value
    :param scale: how much to scale the x axis
    :param multiplier
    :param dna true/false, is sequence a DNA sequence?
    :param t_list list of time points
    :return: None, outputs svg/pdf image of the tree
    """

    if multiplier is None:
        mult = 500
    else:
        mult = multiplier

    if dna:
        dna_prot = 'dna'
        bg_c = {
            'A': 'green',
            'C': 'blue',
            'G': 'black',
            'T': 'red',
            '-': 'grey',
            'X': 'white'
        }

        fg_c = {
            'A': 'black',
            'C': 'black',
            'G': 'black',
            'T': 'black',
            '-': 'black',
            'X': 'white'
        }
    else:
        dna_prot = 'aa'
        bg_c = {
            'K': '#145AFF',
            'R': '#145AFF',
            'H': '#8282D2',
            'E': '#E60A0A',
            'D': '#E60A0A',
            'N': '#00DCDC',
            'Q': '#00DCDC',
            'S': '#FA9600',
            'T': '#FA9600',
            'L': '#0F820F',
            'I': '#0F820F',
            'V': '#0F820F',
            'Y': '#3232AA',
            'F': '#3232AA',
            'W': '#B45AB4',
            'C': '#E6E600',
            'M': '#E6E600',
            'A': '#C8C8C8',
            'G': '#EBEBEB',
            'P': '#DC9682',
            '-': 'grey',
            'X': 'white'
        }

        fg_c = {
            'K': 'black',
            'R': 'black',
            'H': 'black',
            'E': 'black',
            'D': 'black',
            'N': 'black',
            'Q': 'black',
            'S': 'black',
            'T': 'black',
            'L': 'black',
            'I': 'black',
            'V': 'black',
            'Y': 'black',
            'F': 'black',
            'W': 'black',
            'C': 'black',
            'M': 'black',
            'A': 'black',
            'G': 'black',
            'P': 'black',
            '-': 'grey',
            'X': 'white'
        }

    if colours == 3:
        bg_c = None
        fg_c = None

    # outfile3 = str(outfile1.replace(".svg", ".nwk"))

    tstyle = TreeStyle()
    tstyle.force_topology = False
    tstyle.mode = types
    tstyle.scale = scale
    tstyle.min_leaf_separation = 0
    tstyle.optimal_scale_level = 'full'  # 'mid'
    # tstyle.complete_branch_lines_when_necessary = False
    if types == 'c':
        tstyle.root_opening_factor = 0.25

    tstyle.draw_guiding_lines = False
    tstyle.guiding_lines_color = 'slateblue'
    tstyle.show_leaf_name = False
    tstyle.allow_face_overlap = True
    tstyle.show_branch_length = False
    tstyle.show_branch_support = False
    TreeNode(format=0, support=True)
    # tnode = TreeNode()

    if root is not None:
        tree.set_outgroup(root)
    # else:
    #     r = tnode.get_midpoint_outgroup()
    #     print("r", r)
    #     tree.set_outgroup(r)
    time_col = []
    for node in tree.traverse():
        # node.ladderize()
        if node.is_leaf() is True:
            try:
                name = node.name.split("_")
                time = name[field2]
                kind = name[3]
                # print(name)
            except:
                time = 'zero'
                name = node.name
                print("Incorrect name format for ", node.name)

            if size is True:
                try:
                    s = 20 + float(name[field1]) * mult
                except:
                    s = 20
                    print("No frequency information for ", node.name)
            else:
                s = 20

            colour = c_dict[time]
            time_col.append((time, colour))
            nstyle = NodeStyle()
            nstyle["fgcolor"] = colour
            nstyle["size"] = s
            nstyle["hz_line_width"] = 10
            nstyle["vt_line_width"] = 10
            nstyle["hz_line_color"] = colour
            nstyle["vt_line_color"] = 'black'
            nstyle["hz_line_type"] = 0
            nstyle["vt_line_type"] = 0
            node.set_style(nstyle)

            if root is not None and node.name == root:  # place holder in case you want to do something with the root leaf
                print('root is ', node.name)
                # nstyle["shape"] = "square"
                # nstyle["fgcolor"] = "black"
                # nstyle["size"] = s
                # nstyle["shape"] = "circle"
                # node.set_style(nstyle)

            else:
                nstyle["shape"] = "circle"
                node.set_style(nstyle)

            if fasta is not None:
                seq = fasta[str(node.name)]
                seqFace = SequenceFace(seq,
                                       seqtype=dna_prot,
                                       fsize=10,
                                       fg_colors=fg_c,
                                       bg_colors=bg_c,
                                       codon=None,
                                       col_w=40,
                                       alt_col_w=3,
                                       special_col=None,
                                       interactive=True)
                # seqFace = SeqMotifFace(seq=seq, motifs=None, seqtype=dna_prot, gap_format=' ', seq_format='()', scale_factor=20,
                #              height=20, width=50, fgcolor='white', bgcolor='grey', gapcolor='white', )
                # seqFace = SeqMotifFace(seq, seq_format="seq", fgcolor=fg_c, bgcolor=bg_c) #interactive=True

                (tree & node.name).add_face(seqFace, 0, "aligned")

        else:
            nstyle = NodeStyle()
            nstyle["size"] = 0.1
            nstyle["hz_line_width"] = 10
            nstyle["vt_line_width"] = 10
            node.set_style(nstyle)
            continue
    tree.ladderize()
    # tnode.ladderize()
    legendkey = sorted(set(time_col))
    legendkey = [(tp, col) for tp, col in legendkey]
    # legendkey.insert(0, ('Root', 'black'))
    legendkey.append(('', 'white'))

    for tm, clr in legendkey:
        tstyle.legend.add_face(faces.CircleFace(30, clr), column=0)
        tstyle.legend.add_face(faces.TextFace('\t' + tm,
                                              ftype='Arial',
                                              fsize=60,
                                              fgcolor='black',
                                              tight_text=True),
                               column=1)
    if show is True:
        tree.show(tree_style=tstyle)

    tree.render(outfile1, dpi=600, tree_style=tstyle)
Example #6
0
def plot_tree_barplot(tree_file, taxon2mlst, header_list):
    '''

    display one or more barplot

    :param tree_file:
    :param taxon2value_list:
    :param exclude_outgroup:
    :param bw_scale:
    :param barplot2percentage: list of bool to indicates if the number are percentages and the range should be set to 0-100

    :return:
    '''

    import matplotlib.cm as cm
    from matplotlib.colors import rgb2hex
    import matplotlib as mpl

    mlst_list = list(set(taxon2mlst.values()))
    mlst2color = dict(zip(mlst_list, get_spaced_colors(len(mlst_list))))
    mlst2color['-'] = 'white'

    if isinstance(tree_file, Tree):
        t1 = tree_file
    else:
        t1 = Tree(tree_file)

    # Calculate the midpoint node
    R = t1.get_midpoint_outgroup()
    # and set it as tree outgroup
    t1.set_outgroup(R)

    tss = TreeStyle()
    value = 1
    tss.draw_guiding_lines = True
    tss.guiding_lines_color = "gray"
    tss.show_leaf_name = False

    cmap = cm.YlGnBu  #YlOrRd#OrRd

    scale_list = []
    max_value_list = []

    for i, lf in enumerate(t1.iter_leaves()):

        #if taxon2description[lf.name] == 'Pirellula staleyi DSM 6068':
        #    lf.name = 'Pirellula staleyi DSM 6068'
        #    continue
        if i == 0:
            # header

            col_add = 0

            #lf.add_face(n, column, position="aligned")
            n = TextFace('MLST')
            n.margin_top = 1
            n.margin_right = 2
            n.margin_left = 2
            n.margin_bottom = 1
            n.rotation = 90
            n.inner_background.color = "white"
            n.opacity = 1.
            n.hz_align = 2
            n.vt_align = 2

            tss.aligned_header.add_face(n, col_add + 1)

        try:
            #if lf.name in leaf2mlst or int(lf.name) in leaf2mlst:
            n = TextFace(' %s ' % taxon2mlst[int(lf.name)])
            n.inner_background.color = 'white'
            m = TextFace('  ')
            m.inner_background.color = mlst2color[taxon2mlst[int(lf.name)]]
        except:
            n = TextFace(' na ')
            n.inner_background.color = "grey"
            m = TextFace('    ')
            m.inner_background.color = "white"

        n.opacity = 1.
        n.margin_top = 2
        n.margin_right = 2
        n.margin_left = 0
        n.margin_bottom = 2

        m.margin_top = 2
        m.margin_right = 0
        m.margin_left = 2
        m.margin_bottom = 2

        lf.add_face(m, 0, position="aligned")
        lf.add_face(n, 1, position="aligned")

        n = TextFace(lf.name, fgcolor="black", fsize=12, fstyle='italic')
        lf.add_face(n, 0)

    for n in t1.traverse():
        nstyle = NodeStyle()
        if n.support < 1:
            nstyle["fgcolor"] = "black"
            nstyle["size"] = 6
            n.set_style(nstyle)
        else:
            nstyle["fgcolor"] = "red"
            nstyle["size"] = 0
            n.set_style(nstyle)

    return t1, tss
Example #7
0
from ete3 import TreeStyle
from ete3 import EvolTree
from ete3 import faces

tree = EvolTree("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment('data/S_example/alignment_S_measuring_evol.fasta')

print(tree)

print('\n Running free-ratio model with calculation of ancestral sequences...')

tree.run_model('fb_anc')
#tree.link_to_evol_model('/tmp/ete3-codeml/fb_anc/out', 'fb_anc')

I = TreeStyle()
I.force_topology = False
I.draw_aligned_faces_as_table = True
I.draw_guiding_lines = True
I.guiding_lines_type = 2
I.guiding_lines_color = "#CCCCCC"
for n in sorted(tree.get_descendants() + [tree], key=lambda x: x.node_id):
    if n.is_leaf(): continue
    anc_face = faces.SequenceFace(n.sequence, 'aa', fsize=10, bg_colors={})
    I.aligned_foot.add_face(anc_face, 1)
    I.aligned_foot.add_face(
        faces.TextFace('node_id: #%d ' % (n.node_id), fsize=8), 0)
print('display result of bs_anc model, with ancestral amino acid sequences.')
tree.show(tree_style=I)

print('\nThe End.')
        F = faces.TextFace(mynode.name,fsize=20)
        faces.add_face_to_node(F,mynode,0,position="aligned")

#Plot Pie Chart	
ts = TreeStyle()
ts.show_leaf_name = False

ts.layout_fn = phyparts_pie_layout
nstyle = NodeStyle()
nstyle["size"] = 0
for n in plot_tree.traverse():
	n.set_style(nstyle)
	n.img_style["vt_line_width"] = 0

ts.draw_guiding_lines = True
ts.guiding_lines_color = "black"
ts.guiding_lines_type = 0
ts.scale = 30
ts.branch_vertical_margin = 10
plot_tree.convert_to_ultrametric()
plot_tree.ladderize(direction=1)    
my_svg = plot_tree.render(args.svg_name,tree_style=ts,w=595,dpi=300)

if args.show_nodes:
	node_style = TreeStyle()
	node_style.show_leaf_name=False
	node_style.layout_fn = node_text_layout
	plot_tree.show(tree_style=node_style)

     
    
Example #9
0
def plot_phylum_counts(NOG_id,
                       rank='phylum',
                       colapse_low_species_counts=4,
                       remove_unlassified=True):
    '''

    1. get phylum tree
    2. foreach species => get phylum
    3. build phylum2count dictionnary
    3. plot barchart

    # merge eukaryotes into 5 main clades
    # merge virus as a single clade


    ATTENTION: no-rank groups and no-rank species...

    '''

    import MySQLdb
    import os
    from chlamdb.biosqldb import manipulate_biosqldb
    from ete3 import NCBITaxa, Tree, TextFace, TreeStyle, StackedBarFace
    ncbi = NCBITaxa()

    sqlpsw = os.environ['SQLPSW']
    conn = MySQLdb.connect(
        host="localhost",  # your host, usually localhost
        user="******",  # your username
        passwd=sqlpsw,  # your password
        db="eggnog")  # name of the data base
    cursor = conn.cursor()

    sql = 'select * from eggnog.leaf2n_genomes_%s' % rank

    cursor.execute(sql, )
    leaf_taxon2n_species = manipulate_biosqldb.to_dict(cursor.fetchall())

    leaf_taxon2n_species_with_domain = get_NOG_taxonomy(NOG_id, rank)

    sql = 'select phylogeny from eggnog.phylogeny where rank="%s"' % (rank)

    cursor.execute(sql, )
    tree = Tree(cursor.fetchall()[0][0], format=1)

    sql = 'select * from eggnog.taxid2label_%s' % rank
    cursor.execute(sql, )

    taxon_id2scientific_name_and_rank = manipulate_biosqldb.to_dict(
        cursor.fetchall())
    taxon_id2scientific_name_and_rank = {
        str(k): v
        for k, v in taxon_id2scientific_name_and_rank.items()
    }

    tss = TreeStyle()
    tss.draw_guiding_lines = True
    tss.guiding_lines_color = "blue"

    keep = []
    for lf in tree.iter_leaves():
        # n genomes

        if remove_unlassified:
            label = taxon_id2scientific_name_and_rank[str(lf.name)][0]
            if 'unclassified' in label:
                continue

        n_genomes = int(leaf_taxon2n_species[lf.name])
        if n_genomes > colapse_low_species_counts:
            keep.append(lf.name)
    print('number of leaaves:', len(keep))

    tree.prune(keep)

    header_list = ['Rank', 'N genomes', 'N with %s' % NOG_id, 'Percentage']
    for col, header in enumerate(header_list):

        n = TextFace('%s' % (header))
        n.margin_top = 0
        n.margin_right = 1
        n.margin_left = 20
        n.margin_bottom = 1
        n.rotation = 270
        n.hz_align = 2
        n.vt_align = 2
        n.inner_background.color = "white"
        n.opacity = 1.
        tss.aligned_header.add_face(n, col)

    for lf in tree.iter_leaves():
        # n genomes

        n_genomes = int(leaf_taxon2n_species[lf.name])
        if n_genomes <= colapse_low_species_counts:
            continue

        n = TextFace('  %s ' % str(leaf_taxon2n_species[lf.name]))
        n.margin_top = 1
        n.margin_right = 1
        n.margin_left = 0
        n.margin_bottom = 1
        n.fsize = 7
        n.inner_background.color = "white"
        n.opacity = 1.
        lf.add_face(n, 2, position="aligned")

        # n genomes with domain
        try:
            m = TextFace('  %s ' %
                         str(leaf_taxon2n_species_with_domain[lf.name]))
        except:
            m = TextFace('  0 ')
        m.margin_top = 1
        m.margin_right = 1
        m.margin_left = 0
        m.margin_bottom = 1
        m.fsize = 7
        m.inner_background.color = "white"
        m.opacity = 1.
        lf.add_face(m, 3, position="aligned")

        # rank
        ranks = ncbi.get_rank([lf.name])
        try:
            r = ranks[max(ranks.keys())]
        except:
            r = '-'
        n = TextFace('  %s ' % r, fsize=14, fgcolor='red')
        n.margin_top = 1
        n.margin_right = 1
        n.margin_left = 0
        n.margin_bottom = 1
        n.fsize = 7
        n.inner_background.color = "white"
        n.opacity = 1.
        lf.add_face(n, 1, position="aligned")

        # percent with target domain
        try:
            percentage = (float(leaf_taxon2n_species_with_domain[lf.name]) /
                          float(leaf_taxon2n_species[lf.name])) * 100
        except:
            percentage = 0
        m = TextFace('  %s ' % str(round(percentage, 2)))
        m.fsize = 1
        m.margin_top = 1
        m.margin_right = 1
        m.margin_left = 0
        m.margin_bottom = 1
        m.fsize = 7
        m.inner_background.color = "white"
        m.opacity = 1.
        lf.add_face(m, 4, position="aligned")

        b = StackedBarFace([percentage, 100 - percentage],
                           width=100,
                           height=10,
                           colors=["#7fc97f", "white"])
        b.rotation = 0
        b.inner_border.color = "grey"
        b.inner_border.width = 0
        b.margin_right = 15
        b.margin_left = 0
        lf.add_face(b, 5, position="aligned")

        n = TextFace('%s' % taxon_id2scientific_name_and_rank[str(lf.name)][0],
                     fgcolor="black",
                     fsize=9)  # , fstyle = 'italic'

        lf.name = " %s (%s)" % (taxon_id2scientific_name_and_rank[str(
            lf.name)][0], str(lf.name))
        n.margin_right = 10
        lf.add_face(n, 0)

    tss.show_leaf_name = False

    for node in tree.traverse("postorder"):
        try:
            r = taxon_id2scientific_name_and_rank[str(node.name)][1]
        except:
            pass
        try:
            if r in ['phylum', 'superkingdom', 'class', 'subphylum'
                     ] or taxon_id2scientific_name_and_rank[str(
                         node.name)][0] in ['FCB group']:

                hola = TextFace(
                    "%s" %
                    (taxon_id2scientific_name_and_rank[str(node.name)][0]))
                node.add_face(hola, column=0, position="branch-top")
        except:
            pass
    return tree, tss
Example #10
0
            circular_style = TreeStyle()
            circular_style.show_leaf_name = False
            circular_style.show_branch_length = True
            circular_style.show_branch_support = True
            circular_style.scale = 75
            circular_style.tree_width = 50
            #circular_style.rotation = 90
            #circular_style.extra_branch_line_type=(0) 
            #circular_style.guiding_lines_type= (0)
            #circular_style.title.add_face(TextFace(File, fsize=25), column=0)
            circular_style.layout_fn = layout
            t.render(adres+"/out/"+File[:-4]+".png", tree_style=circular_style)
            circular_style.mode = "r" # draw tree in circular mode
            circular_style.extra_branch_line_type=(2) 
            circular_style.guiding_lines_type= (2)
            circular_style.guiding_lines_color =("red")
            for n in t.traverse():
			   nstyle = NodeStyle()
			   nstyle["fgcolor"] = "red"
			   nstyle["size"] = 15
			   n.set_style(nstyle) 
			   #N = AttrFace("name", fsize=30)
               #faces.add_face_to_node(N, node, 0, position="aligned")
            circular_style.legend.add_face =(TextFace("0.5 support"), column=1)
            circular_style.legend.add_face =(CircleFace(10, "red"), column=0)
            circular_style.layout_fn = layout
            circular_style.legend.add_face(TextFace("0.5 support"), column=1)
            circular_style.title.add_face(TextFace(File, fsize=40), column=0)
            TextFace_=TextFace(text, ftype='Verdana', fsize=10, fgcolor='black', penwidth=0, fstyle='normal', tight_text=False, bold=False)
            t.render(adres+"/out/"+File[:-4]+"_c.png", tree_style=circular_style)
Example #11
0
from ete3 import faces


tree = EvolTree ("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment ('data/S_example/alignment_S_measuring_evol.fasta')

print tree

print '\n Running free-ratio model with calculation of ancestral sequences...'

tree.run_model ('fb_anc')
#tree.link_to_evol_model('/tmp/ete3-codeml/fb_anc/out', 'fb_anc')

I = TreeStyle()
I.force_topology             = False
I.draw_aligned_faces_as_table = True
I.draw_guiding_lines = True
I.guiding_lines_type = 2
I.guiding_lines_color = "#CCCCCC"
for n in sorted (tree.get_descendants()+[tree],
                 key=lambda x: x.node_id):
    if n.is_leaf(): continue
    anc_face = faces.SequenceFace (n.sequence, 'aa', fsize=10, bg_colors={})
    I.aligned_foot.add_face(anc_face, 1)
    I.aligned_foot.add_face(faces.TextFace('node_id: #%d '%(n.node_id),
                                           fsize=8), 0)
print 'display result of bs_anc model, with ancestral amino acid sequences.'
tree.show(tree_style=I)

print '\nThe End.'
Example #12
0
def plot_tree_stacked_barplot(
        tree_file,
        taxon2value_list_barplot=False,
        header_list=False,  # header stackedbarplots
        taxon2set2value_heatmap=False,
        taxon2label=False,
        header_list2=False,  # header counts columns
        biodb=False,
        column_scale=True,
        general_max=False,
        header_list3=False,
        set2taxon2value_list_simple_barplot=False,
        set2taxon2value_list_simple_barplot_counts=True,
        rotate=False,
        taxon2description=False):
    '''

    taxon2value_list_barplot list of lists:
    [[bar1_part1, bar1_part2,...],[bar2_part1, bar2_part2]]
    valeures de chaque liste transformes en pourcentages

    :param tree_file:
    :param taxon2value_list:
    :param biodb:
    :param exclude_outgroup:
    :param bw_scale:
    :return:
    '''

    if biodb:
        from chlamdb.biosqldb import manipulate_biosqldb
        server, db = manipulate_biosqldb.load_db(biodb)

        taxon2description = manipulate_biosqldb.taxon_id2genome_description(
            server, biodb, filter_names=True)

    t1 = Tree(tree_file)

    # Calculate the midpoint node
    R = t1.get_midpoint_outgroup()
    # and set it as tree outgroup
    t1.set_outgroup(R)

    colors2 = [
        "red", "#FFFF00", "#58FA58", "#819FF7", "#F781F3", "#2E2E2E",
        "#F7F8E0", 'black'
    ]
    colors = [
        "#7fc97f", "#386cb0", "#fdc086", "#ffffb3", "#fdb462", "#f0027f",
        "#F7F8E0", 'black'
    ]  # fdc086ff 386cb0ff f0027fff

    tss = TreeStyle()
    tss.draw_guiding_lines = True
    tss.guiding_lines_color = "gray"
    tss.show_leaf_name = False
    if column_scale and header_list2:
        import matplotlib.cm as cm
        from matplotlib.colors import rgb2hex
        import matplotlib as mpl
        column2scale = {}
        col_n = 0
        for column in header_list2:
            values = taxon2set2value_heatmap[column].values()
            #print values
            if min(values) == max(values):
                min_val = 0
                max_val = 1.5 * max(values)
            else:
                min_val = min(values)
                max_val = max(values)
            #print 'min-max', min_val, max_val
            norm = mpl.colors.Normalize(vmin=min_val, vmax=max_val)  # *1.1
            if col_n < 4:
                cmap = cm.OrRd  #
            else:
                cmap = cm.YlGnBu  #PuBu#OrRd

            m = cm.ScalarMappable(norm=norm, cmap=cmap)

            column2scale[column] = [m, float(max_val)]  # *0.7
            col_n += 1

    for i, lf in enumerate(t1.iter_leaves()):

        #if taxon2description[lf.name] == 'Pirellula staleyi DSM 6068':
        #    lf.name = 'Pirellula staleyi DSM 6068'
        #    continue
        if i == 0:

            if taxon2label:
                n = TextFace('  ')
                n.margin_top = 1
                n.margin_right = 1
                n.margin_left = 20
                n.margin_bottom = 1
                n.hz_align = 2
                n.vt_align = 2
                n.rotation = 270
                n.inner_background.color = "white"
                n.opacity = 1.

                tss.aligned_header.add_face(n, 0)
                col_add = 1
            else:
                col_add = 1
            if header_list:
                for col, header in enumerate(header_list):

                    n = TextFace('%s' % (header))
                    n.margin_top = 0
                    n.margin_right = 1
                    n.margin_left = 20
                    n.margin_bottom = 1
                    n.rotation = 270
                    n.hz_align = 2
                    n.vt_align = 2
                    n.inner_background.color = "white"
                    n.opacity = 1.
                    tss.aligned_header.add_face(n, col + col_add)
                col_add += col + 1

            if header_list3:
                #print 'header_list 3!'
                col_tmp = 0
                for header in header_list3:
                    n = TextFace('%s' % (header))
                    n.margin_top = 1
                    n.margin_right = 1
                    n.margin_left = 20
                    n.margin_bottom = 1
                    n.rotation = 270
                    n.hz_align = 2
                    n.vt_align = 2
                    n.inner_background.color = "white"
                    n.opacity = 1.

                    if set2taxon2value_list_simple_barplot_counts:
                        if col_tmp == 0:
                            col_tmp += 1
                        tss.aligned_header.add_face(n, col_tmp + 1 + col_add)
                        n = TextFace('       ')
                        tss.aligned_header.add_face(n, col_tmp + col_add)
                        col_tmp += 2
                    else:
                        tss.aligned_header.add_face(n, col_tmp + col_add)
                        col_tmp += 1
                if set2taxon2value_list_simple_barplot_counts:
                    col_add += col_tmp
                else:
                    col_add += col_tmp

            if header_list2:
                for col, header in enumerate(header_list2):
                    n = TextFace('%s' % (header))
                    n.margin_top = 1
                    n.margin_right = 1
                    n.margin_left = 20
                    n.margin_bottom = 1
                    n.rotation = 270
                    n.hz_align = 2
                    n.vt_align = 2
                    n.inner_background.color = "white"
                    n.opacity = 1.
                    tss.aligned_header.add_face(n, col + col_add)
                col_add += col + 1

        if taxon2label:
            try:
                n = TextFace('%s' % taxon2label[lf.name])
            except:
                try:
                    n = TextFace('%s' % taxon2label[int(lf.name)])
                except:
                    n = TextFace('-')
            n.margin_top = 1
            n.margin_right = 1
            n.margin_left = 20
            n.margin_bottom = 1
            n.inner_background.color = "white"
            n.opacity = 1.
            if rotate:
                n.rotation = 270
            lf.add_face(n, 1, position="aligned")
            col_add = 2
        else:
            col_add = 2

        if taxon2value_list_barplot:

            try:
                val_list_of_lists = taxon2value_list_barplot[lf.name]
            except:
                val_list_of_lists = taxon2value_list_barplot[int(lf.name)]

            #col_count = 0
            for col, value_list in enumerate(val_list_of_lists):

                total = float(sum(value_list))
                percentages = [(i / total) * 100 for i in value_list]
                if col % 3 == 0:
                    col_list = colors2
                else:
                    col_list = colors
                b = StackedBarFace(percentages,
                                   width=150,
                                   height=18,
                                   colors=col_list[0:len(percentages)])
                b.rotation = 0
                b.inner_border.color = "white"
                b.inner_border.width = 0
                b.margin_right = 5
                b.margin_left = 5
                if rotate:
                    b.rotation = 270
                lf.add_face(b, col + col_add, position="aligned")
                #col_count+=1

            col_add += col + 1

        if set2taxon2value_list_simple_barplot:
            col_list = [
                '#fc8d59', '#91bfdb', '#99d594', '#c51b7d', '#f1a340',
                '#999999'
            ]
            color_i = 0
            col = 0
            for one_set in header_list3:
                if color_i > 5:
                    color_i = 0
                color = col_list[color_i]
                color_i += 1
                # values for all taxons
                values_lists = [
                    float(i) for i in
                    set2taxon2value_list_simple_barplot[one_set].values()
                ]
                #print values_lists
                #print one_set
                value = set2taxon2value_list_simple_barplot[one_set][lf.name]

                if set2taxon2value_list_simple_barplot_counts:
                    if isinstance(value, float):
                        a = TextFace(" %s " % str(round(value, 2)))
                    else:
                        a = TextFace(" %s " % str(value))
                    a.margin_top = 1
                    a.margin_right = 2
                    a.margin_left = 5
                    a.margin_bottom = 1
                    if rotate:
                        a.rotation = 270
                    lf.add_face(a, col + col_add, position="aligned")

                #print 'value and max', value, max(values_lists)
                fraction_biggest = (float(value) / max(values_lists)) * 100
                fraction_rest = 100 - fraction_biggest

                #print 'fractions', fraction_biggest, fraction_rest
                b = StackedBarFace([fraction_biggest, fraction_rest],
                                   width=100,
                                   height=15,
                                   colors=[color, 'white'])
                b.rotation = 0
                b.inner_border.color = "grey"
                b.inner_border.width = 0
                b.margin_right = 15
                b.margin_left = 0
                if rotate:
                    b.rotation = 270
                if set2taxon2value_list_simple_barplot_counts:
                    if col == 0:
                        col += 1
                    lf.add_face(b, col + 1 + col_add, position="aligned")
                    col += 2
                else:
                    lf.add_face(b, col + col_add, position="aligned")
                    col += 1
            if set2taxon2value_list_simple_barplot_counts:
                col_add += col

            else:
                col_add += col

        if taxon2set2value_heatmap:
            i = 0
            #if not taxon2label:
            #    col_add-=1
            for col2, head in enumerate(header_list2):

                col_name = header_list2[i]
                try:
                    value = taxon2set2value_heatmap[col_name][str(lf.name)]
                except:
                    try:
                        value = taxon2set2value_heatmap[col_name][round(
                            float(lf.name), 2)]
                    except:
                        value = 0
                if header_list2[i] == 'duplicates':
                    print('dupli', lf.name, value)
                #print 'val----------------', value
                if int(value) > 0:
                    if int(value) >= 10 and int(value) < 100:
                        n = TextFace('%4i' % value)
                    elif int(value) >= 100:
                        n = TextFace('%3i' % value)
                    else:

                        n = TextFace('%5i' % value)

                    n.margin_top = 1
                    n.margin_right = 2
                    n.margin_left = 5
                    n.margin_bottom = 1
                    n.hz_align = 1
                    n.vt_align = 1
                    if rotate:
                        n.rotation = 270
                    n.inner_background.color = rgb2hex(
                        column2scale[col_name][0].to_rgba(
                            float(value)))  #"orange"
                    #print 'xaxaxaxaxa', value,
                    if float(value) > column2scale[col_name][1]:

                        n.fgcolor = 'white'
                    n.opacity = 1.
                    n.hz_align = 1
                    n.vt_align = 1
                    lf.add_face(n, col2 + col_add, position="aligned")
                    i += 1
                else:
                    n = TextFace('')
                    n.margin_top = 1
                    n.margin_right = 1
                    n.margin_left = 5
                    n.margin_bottom = 1
                    n.inner_background.color = "white"
                    n.opacity = 1.
                    if rotate:
                        n.rotation = 270
                    lf.add_face(n, col2 + col_add, position="aligned")
                    i += 1

        #lf.name = taxon2description[lf.name]
        n = TextFace(taxon2description[lf.name],
                     fgcolor="black",
                     fsize=12,
                     fstyle='italic')
        lf.add_face(n, 0)

    for n in t1.traverse():
        nstyle = NodeStyle()

        if n.support < 1:
            nstyle["fgcolor"] = "black"
            nstyle["size"] = 6
            n.set_style(nstyle)
        else:
            nstyle["fgcolor"] = "red"
            nstyle["size"] = 0
            n.set_style(nstyle)

    return t1, tss
Example #13
0
def plot_heat_tree(tree_file,
                   biodb="chlamydia_04_16",
                   exclude_outgroup=False,
                   bw_scale=True):
    from chlamdb.biosqldb import manipulate_biosqldb
    import matplotlib.cm as cm
    from matplotlib.colors import rgb2hex
    import matplotlib as mpl

    server, db = manipulate_biosqldb.load_db(biodb)

    sql_biodatabase_id = 'select biodatabase_id from biodatabase where name="%s"' % biodb
    db_id = server.adaptor.execute_and_fetchall(sql_biodatabase_id, )[0][0]
    if type(tree_file) == str:
        t1 = Tree(tree_file)
        try:
            R = t1.get_midpoint_outgroup()
            #print 'root', R
            # and set it as tree outgroup
            t1.set_outgroup(R)
        except:
            pass
    elif isinstance(tree_file, Tree):
        t1 = tree_file
    else:
        IOError('Unkown tree format')
    tss = TreeStyle()
    tss.draw_guiding_lines = True
    tss.guiding_lines_color = "gray"
    tss.show_leaf_name = False

    #print "tree", t1

    sql1 = 'select taxon_id, description from bioentry where biodatabase_id=%s and description not like "%%%%plasmid%%%%"' % db_id
    sql2 = 'select t2.taxon_id, t1.GC from genomes_info_%s as t1 inner join bioentry as t2 ' \
           ' on t1.accession=t2.accession where t2.biodatabase_id=%s and t1.description not like "%%%%plasmid%%%%";' % (biodb, db_id)
    sql3 = 'select t2.taxon_id, t1.genome_size from genomes_info_%s as t1 ' \
           ' inner join bioentry as t2 on t1.accession=t2.accession ' \
           ' where t2.biodatabase_id=%s and t1.description not like "%%%%plasmid%%%%";' % (biodb, db_id)
    sql4 = 'select t2.taxon_id,percent_non_coding from genomes_info_%s as t1 ' \
           ' inner join bioentry as t2 on t1.accession=t2.accession ' \
           ' where t2.biodatabase_id=%s and t1.description not like "%%%%plasmid%%%%";' % (biodb, db_id)

    sql_checkm_completeness = 'select taxon_id, completeness from custom_tables.checkm_%s;' % biodb
    sql_checkm_contamination = 'select taxon_id,contamination from custom_tables.checkm_%s;' % biodb

    try:
        taxon_id2completeness = manipulate_biosqldb.to_dict(
            server.adaptor.execute_and_fetchall(sql_checkm_completeness))
        taxon_id2contamination = manipulate_biosqldb.to_dict(
            server.adaptor.execute_and_fetchall(sql_checkm_contamination))
    except:
        taxon_id2completeness = False
    #taxon2description = manipulate_biosqldb.to_dict(server.adaptor.execute_and_fetchall(sql1,))

    taxon2description = manipulate_biosqldb.taxon_id2genome_description(
        server, biodb, filter_names=True)

    taxon2gc = manipulate_biosqldb.to_dict(
        server.adaptor.execute_and_fetchall(sql2, ))
    taxon2genome_size = manipulate_biosqldb.to_dict(
        server.adaptor.execute_and_fetchall(sql3, ))
    taxon2coding_density = manipulate_biosqldb.to_dict(
        server.adaptor.execute_and_fetchall(sql4, ))

    my_taxons = [lf.name for lf in t1.iter_leaves()]

    # Calculate the midpoint node

    if exclude_outgroup:
        excluded = str(list(t1.iter_leaves())[0].name)
        my_taxons.pop(my_taxons.index(excluded))

    genome_sizes = [float(taxon2genome_size[i]) for i in my_taxons]
    gc_list = [float(taxon2gc[i]) for i in my_taxons]
    fraction_list = [float(taxon2coding_density[i]) for i in my_taxons]

    value = 1

    max_genome_size = max(genome_sizes)  #3424182#
    max_gc = max(gc_list)  #48.23

    cmap = cm.YlGnBu  #YlOrRd#OrRd

    norm = mpl.colors.Normalize(vmin=min(genome_sizes) - 100000,
                                vmax=max(genome_sizes))
    m1 = cm.ScalarMappable(norm=norm, cmap=cmap)
    norm = mpl.colors.Normalize(vmin=min(gc_list), vmax=max(gc_list))
    m2 = cm.ScalarMappable(norm=norm, cmap=cmap)
    norm = mpl.colors.Normalize(vmin=min(fraction_list),
                                vmax=max(fraction_list))
    m3 = cm.ScalarMappable(norm=norm, cmap=cmap)

    for i, lf in enumerate(t1.iter_leaves()):
        #if taxon2description[lf.name] == 'Pirellula staleyi DSM 6068':
        #    lf.name = 'Pirellula staleyi DSM 6068'
        #    continue
        if i == 0:
            n = TextFace('Size (Mbp)')
            n.rotation = -25
            n.margin_top = 1
            n.margin_right = 1
            n.margin_left = 20
            n.margin_bottom = 1
            n.inner_background.color = "white"
            n.opacity = 1.
            #lf.add_face(n, 3, position="aligned")
            tss.aligned_header.add_face(n, 3)
            n = TextFace('GC (%)')
            n.rotation = -25
            n.margin_top = 1
            n.margin_right = 1
            n.margin_left = 20
            n.margin_bottom = 1
            n.inner_background.color = "white"
            n.opacity = 1.
            #lf.add_face(n, 5, position="aligned")
            tss.aligned_header.add_face(n, 5)
            n = TextFace('')
            #lf.add_face(n, 2, position="aligned")
            tss.aligned_header.add_face(n, 2)
            #lf.add_face(n, 4, position="aligned")
            tss.aligned_header.add_face(n, 4)
            n = TextFace('Non coding (%)')
            n.margin_top = 1
            n.margin_right = 1
            n.margin_left = 20
            n.margin_bottom = 1
            n.inner_background.color = "white"
            n.opacity = 1.
            n.rotation = -25
            #lf.add_face(n, 7, position="aligned")
            tss.aligned_header.add_face(n, 7)
            n = TextFace('')
            #lf.add_face(n, 6, position="aligned")
            tss.aligned_header.add_face(n, 6)

            if taxon_id2completeness:
                n = TextFace('Completeness (%)')
                n.margin_top = 1
                n.margin_right = 1
                n.margin_left = 20
                n.margin_bottom = 1
                n.inner_background.color = "white"
                n.opacity = 1.
                n.rotation = -25
                #lf.add_face(n, 7, position="aligned")
                tss.aligned_header.add_face(n, 9)
                n = TextFace('')
                #lf.add_face(n, 6, position="aligned")
                tss.aligned_header.add_face(n, 8)

                n = TextFace('Contamination (%)')
                n.margin_top = 1
                n.margin_right = 1
                n.margin_left = 20
                n.margin_bottom = 1
                n.inner_background.color = "white"
                n.opacity = 1.
                n.rotation = -25
                #lf.add_face(n, 7, position="aligned")
                tss.aligned_header.add_face(n, 11)
                n = TextFace('')
                #lf.add_face(n, 6, position="aligned")
                tss.aligned_header.add_face(n, 10)

        value += 1

        #print '------ %s' % lf.name
        if exclude_outgroup and i == 0:
            lf.name = taxon2description[lf.name]
            #print '#######################'
            continue

        n = TextFace(
            '  %s ' %
            str(round(taxon2genome_size[lf.name] / float(1000000), 2)))
        n.margin_top = 1
        n.margin_right = 1
        n.margin_left = 0
        n.margin_bottom = 1
        n.fsize = 7
        n.inner_background.color = "white"
        n.opacity = 1.

        lf.add_face(n, 2, position="aligned")
        #if max_genome_size > 3424182:
        #    max_genome_size = 3424182
        fraction_biggest = (float(taxon2genome_size[lf.name]) /
                            max_genome_size) * 100
        fraction_rest = 100 - fraction_biggest
        if taxon2description[lf.name] == 'Rhabdochlamydia helveticae T3358':
            col = '#fc8d59'
        else:
            if not bw_scale:
                col = rgb2hex(m1.to_rgba(float(
                    taxon2genome_size[lf.name])))  # 'grey'
            else:
                col = '#fc8d59'

        b = StackedBarFace([fraction_biggest, fraction_rest],
                           width=100,
                           height=9,
                           colors=[col, 'white'])
        b.rotation = 0
        b.inner_border.color = "black"
        b.inner_border.width = 0
        b.margin_right = 15
        b.margin_left = 0
        lf.add_face(b, 3, position="aligned")

        fraction_biggest = (float(taxon2gc[lf.name]) / max_gc) * 100
        fraction_rest = 100 - fraction_biggest
        if taxon2description[lf.name] == 'Rhabdochlamydia helveticae T3358':
            col = '#91bfdb'
        else:
            if not bw_scale:
                col = rgb2hex(m2.to_rgba(float(taxon2gc[lf.name])))
            else:
                col = '#91bfdb'
        b = StackedBarFace([fraction_biggest, fraction_rest],
                           width=100,
                           height=9,
                           colors=[col, 'white'])
        b.rotation = 0
        b.inner_border.color = "black"
        b.inner_border.width = 0
        b.margin_left = 0
        b.margin_right = 15

        lf.add_face(b, 5, position="aligned")
        n = TextFace('  %s ' % str(round(float(taxon2gc[lf.name]), 2)))
        n.margin_top = 1
        n.margin_right = 0
        n.margin_left = 0
        n.margin_bottom = 1
        n.fsize = 7
        n.inner_background.color = "white"
        n.opacity = 1.
        lf.add_face(n, 4, position="aligned")

        if taxon2description[lf.name] == 'Rhabdochlamydia helveticae T3358':
            col = '#99d594'
        else:
            if not bw_scale:
                col = rgb2hex(m3.to_rgba(float(taxon2coding_density[lf.name])))
            else:
                col = '#99d594'
        n = TextFace('  %s ' % str(float(taxon2coding_density[lf.name])))
        n.margin_top = 1
        n.margin_right = 0
        n.margin_left = 0
        n.margin_right = 0
        n.margin_bottom = 1
        n.fsize = 7
        n.inner_background.color = "white"
        n.opacity = 1.
        lf.add_face(n, 6, position="aligned")
        fraction = (float(taxon2coding_density[lf.name]) /
                    max(taxon2coding_density.values())) * 100
        fraction_rest = ((max(taxon2coding_density.values()) -
                          taxon2coding_density[lf.name]) /
                         float(max(taxon2coding_density.values()))) * 100
        #print 'fraction, rest', fraction, fraction_rest
        b = StackedBarFace(
            [fraction, fraction_rest],
            width=100,
            height=9,
            colors=[col, 'white'
                    ])  # 1-round(float(taxon2coding_density[lf.name]), 2)
        b.rotation = 0
        b.margin_right = 1
        b.inner_border.color = "black"
        b.inner_border.width = 0
        b.margin_left = 5
        lf.add_face(b, 7, position="aligned")

        if taxon_id2completeness:
            n = TextFace('  %s ' % str(float(taxon_id2completeness[lf.name])))
            n.margin_top = 1
            n.margin_right = 0
            n.margin_left = 0
            n.margin_right = 0
            n.margin_bottom = 1
            n.fsize = 7
            n.inner_background.color = "white"
            n.opacity = 1.
            lf.add_face(n, 8, position="aligned")
            fraction = float(taxon_id2completeness[lf.name])
            fraction_rest = 100 - fraction
            #print 'fraction, rest', fraction, fraction_rest
            b = StackedBarFace(
                [fraction, fraction_rest],
                width=100,
                height=9,
                colors=["#d7191c", 'white'
                        ])  # 1-round(float(taxon2coding_density[lf.name]), 2)
            b.rotation = 0
            b.margin_right = 1
            b.inner_border.color = "black"
            b.inner_border.width = 0
            b.margin_left = 5
            lf.add_face(b, 9, position="aligned")

            n = TextFace('  %s ' % str(float(taxon_id2contamination[lf.name])))
            n.margin_top = 1
            n.margin_right = 0
            n.margin_left = 0
            n.margin_right = 0
            n.margin_bottom = 1
            n.fsize = 7
            n.inner_background.color = "white"
            n.opacity = 1.
            lf.add_face(n, 10, position="aligned")
            fraction = float(taxon_id2contamination[lf.name])
            fraction_rest = 100 - fraction
            #print 'fraction, rest', fraction, fraction_rest
            b = StackedBarFace(
                [fraction, fraction_rest],
                width=100,
                height=9,
                colors=["black", 'white'
                        ])  # 1-round(float(taxon2coding_density[lf.name]), 2)
            b.rotation = 0
            b.margin_right = 1
            b.inner_border.color = "black"
            b.inner_border.width = 0
            b.margin_left = 5
            lf.add_face(b, 11, position="aligned")

            #lf.name = taxon2description[lf.name]
        n = TextFace(taxon2description[lf.name],
                     fgcolor="black",
                     fsize=9,
                     fstyle='italic')
        n.margin_right = 30
        lf.add_face(n, 0)

    for n in t1.traverse():
        nstyle = NodeStyle()
        if n.support < 1:
            nstyle["fgcolor"] = "black"
            nstyle["size"] = 6
            n.set_style(nstyle)
        else:
            nstyle["fgcolor"] = "red"
            nstyle["size"] = 0
            n.set_style(nstyle)

    return t1, tss
Example #14
0
def plot_tree_text_metadata(tree_file, header2taxon2text, ordered_header_list,
                            biodb):

    from chlamdb.biosqldb import manipulate_biosqldb
    server, db = manipulate_biosqldb.load_db(biodb)

    t1 = Tree(tree_file)

    taxon2description = manipulate_biosqldb.taxon_id2genome_description(
        server, biodb, filter_names=True)

    # Calculate the midpoint node
    R = t1.get_midpoint_outgroup()
    # and set it as tree outgroup
    t1.set_outgroup(R)
    tss = TreeStyle()
    tss.draw_guiding_lines = True
    tss.guiding_lines_color = "gray"
    tss.show_leaf_name = False

    for i, leaf in enumerate(t1.iter_leaves()):

        # first leaf, add headers
        if i == 0:
            for column, header in enumerate(ordered_header_list):

                n = TextFace('%s' % (header))
                n.margin_top = 0
                n.margin_right = 1
                n.margin_left = 20
                n.margin_bottom = 1
                n.rotation = 270
                n.hz_align = 2
                n.vt_align = 2
                n.inner_background.color = "white"
                n.opacity = 1.
                tss.aligned_header.add_face(n, column)
        for column, header in enumerate(ordered_header_list):
            text = header2taxon2text[header][int(leaf.name)]
            n = TextFace('%s' % text)
            n.margin_top = 1
            n.margin_right = 1
            n.margin_left = 5
            n.margin_bottom = 1
            n.inner_background.color = "white"
            n.opacity = 1.
            #n.rotation = 270
            leaf.add_face(n, column + 1, position="aligned")
        # rename leaf (taxon_id => description)
        n = TextFace(taxon2description[leaf.name],
                     fgcolor="black",
                     fsize=12,
                     fstyle='italic')
        leaf.add_face(n, 0)

    for n in t1.traverse():
        # rename leaf

        nstyle = NodeStyle()

        if n.support < 1:
            nstyle["fgcolor"] = "black"
            nstyle["size"] = 6
            n.set_style(nstyle)
        else:
            nstyle["fgcolor"] = "red"
            nstyle["size"] = 0
            n.set_style(nstyle)

    return t1, tss
Example #15
0
def plot_heatmap_tree_locus(biodb,
                            tree_file,
                            taxid2count,
                            taxid2identity=False,
                            taxid2locus=False,
                            reference_taxon=False,
                            n_paralogs_barplot=False):
    '''

    plot tree and associated heatmap with count of homolgs
    optional:
        - add identity of closest homolog
        - add locus tag of closest homolog

    '''

    from chlamdb.biosqldb import manipulate_biosqldb

    server, db = manipulate_biosqldb.load_db(biodb)

    taxid2organism = manipulate_biosqldb.taxon_id2genome_description(
        server, biodb, True)

    t1 = Tree(tree_file)
    ts = TreeStyle()
    ts.draw_guiding_lines = True
    ts.guiding_lines_color = "gray"
    # Calculate the midpoint node
    R = t1.get_midpoint_outgroup()
    # and set it as tree outgroup
    t1.set_outgroup(R)

    leaf_number = 0

    for lf in t1.iter_leaves():

        if str(lf.name) not in taxid2count:
            taxid2count[str(lf.name)] = 0

    max_count = max([taxid2count[str(lf.name)] for lf in t1.iter_leaves()])

    for i, lf in enumerate(t1.iter_leaves()):

        # top leaf, add header
        if i == 0:

            n = TextFace('Number of homologs')
            n.margin_top = 1
            n.margin_right = 1
            n.margin_left = 20
            n.margin_bottom = 1
            n.inner_background.color = "white"
            n.opacity = 1.
            n.rotation = -25
            #lf.add_face(n, 7, position="aligned")
            ts.aligned_header.add_face(n, 1)

            if taxid2identity:
                n = TextFace('Protein identity')
                n.margin_top = 1
                n.margin_right = 1
                n.margin_left = 20
                n.margin_bottom = 1
                n.inner_background.color = "white"
                n.opacity = 1.
                n.rotation = -25
                #lf.add_face(n, 7, position="aligned")
                ts.aligned_header.add_face(n, 2)
            if taxid2locus:
                n = TextFace('Locus tag')
                n.margin_top = 1
                n.margin_right = 1
                n.margin_left = 20
                n.margin_bottom = 1
                n.inner_background.color = "white"
                n.opacity = 1.
                n.rotation = -25
                #lf.add_face(n, 7, position="aligned")
                ts.aligned_header.add_face(n, 3)

        leaf_number += 1

        lf.branch_vertical_margin = 0

        data = [taxid2count[str(lf.name)]]

        # possibility to add one or more columns
        for col, value in enumerate(data):
            col_index = col
            if value > 0:
                n = TextFace(' %s ' % str(value))
                n.margin_top = 2

                n.margin_right = 2
                if col == 0:
                    n.margin_left = 20
                else:
                    n.margin_left = 2
                n.margin_bottom = 2
                n.inner_background.color = "white"  # #81BEF7
                n.opacity = 1.
                lf.add_face(n, col, position="aligned")

            else:
                n = TextFace(' %s ' % str(value))
                n.margin_top = 2
                n.margin_right = 2
                if col == 0:
                    n.margin_left = 20
                else:
                    n.margin_left = 2
                n.margin_bottom = 2
                n.inner_background.color = "white"
                n.opacity = 1.
                lf.add_face(n, col, position="aligned")
        # optionally indicate number of paralogs as a barplot
        if n_paralogs_barplot:
            col_index += 1
            percent = (float(value) / max_count) * 100
            n = StackedBarFace([percent, 100 - percent],
                               width=150,
                               height=18,
                               colors=['#6699ff', 'white'],
                               line_color='white')
            n.rotation = 0
            n.inner_border.color = "white"
            n.inner_border.width = 0
            n.margin_right = 15
            n.margin_left = 0
            lf.add_face(n, col + 1, position="aligned")

        # optionally add additionnal column with identity
        if taxid2identity:
            import matplotlib.cm as cm
            from matplotlib.colors import rgb2hex
            import matplotlib as mpl

            norm = mpl.colors.Normalize(vmin=0, vmax=100)
            cmap = cm.OrRd
            m = cm.ScalarMappable(norm=norm, cmap=cmap)

            try:
                if round(taxid2identity[str(lf.name)], 2) != 100:
                    value = "%.2f" % round(taxid2identity[str(lf.name)], 2)
                else:
                    value = "%.1f" % round(taxid2identity[str(lf.name)], 2)
            except:
                value = '-'
            if str(lf.name) == str(reference_taxon):
                value = '         '
            n = TextFace(' %s ' % value)
            n.margin_top = 2
            n.margin_right = 2
            n.margin_left = 20
            n.margin_bottom = 2
            if not value.isspace() and value is not '-':
                n.inner_background.color = rgb2hex(m.to_rgba(float(value)))
                if float(value) > 82:
                    n.fgcolor = 'white'
            n.opacity = 1.
            if str(lf.name) == str(reference_taxon):
                n.inner_background.color = '#800000'

            lf.add_face(n, col_index + 1, position="aligned")
        # optionaly add column with locus name
        if taxid2locus:
            try:
                value = str(taxid2locus[str(lf.name)])
            except:
                value = '-'
            n = TextFace(' %s ' % value)
            n.margin_top = 2
            n.margin_right = 2
            n.margin_left = 2
            n.margin_bottom = 2
            if str(lf.name) != str(reference_taxon):
                n.inner_background.color = "white"
            else:
                n.fgcolor = '#ff0000'
                n.inner_background.color = "white"
            n.opacity = 1.
            lf.add_face(n, col_index + 2, position="aligned")
        lf.name = taxid2organism[str(lf.name)]

    return t1, leaf_number, ts