Exemple #1
0
def add_branch_text(tree, tree_style, node_dict):
    root_node = tree & 'root'
    for node in tree.traverse():
        if node is root_node:
            continue
        T1 = TextFace(node.name, ftype="Monaco", fsize=10)
        T1.hz_align = 0
        node.add_face(T1, 0, 'branch-top')
        T2 = TextFace('%s%%' % float_trans(node_dict[node.name].profile * 100), ftype="Monaco", fsize=10)
        T2.hz_align = 0
        node.add_face(T2, 0, 'branch-bottom')
        # print node_dict[node.name].size
        node.dist = node_dict[node.name].branch_length
        tree_style.scale = 1
 def my_layout(node):
     circle_color = 'lightgray' if colormap is None or node.name not in colormap else colormap[
         node.name]
     text_color = 'black'
     if isinstance(circle_color, str):
         C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
                        color=circle_color,
                        label={
                            'text': str(node.frequency),
                            'color': text_color
                        } if node.frequency > 0 else None)
         C.rotation = -90
         C.hz_align = 1
         faces.add_face_to_node(C, node, 0)
     else:
         P = PieChartFace(
             [100 * x / node.frequency for x in circle_color.values()],
             2 * 10 * scipy.sqrt(node.frequency),
             2 * 10 * scipy.sqrt(node.frequency),
             colors=[(color if color != 'None' else 'lightgray')
                     for color in list(circle_color.keys())],
             line_color=None)
         T = TextFace(' '.join(
             [str(x) for x in list(circle_color.values())]),
                      tight_text=True)
         T.hz_align = 1
         T.rotation = -90
         faces.add_face_to_node(P, node, 0, position='branch-right')
         faces.add_face_to_node(T, node, 1, position='branch-right')
     if idlabel:
         T = TextFace(node.name, tight_text=True, fsize=6)
         T.rotation = -90
         T.hz_align = 1
         faces.add_face_to_node(
             T,
             node,
             1 if isinstance(circle_color, str) else 2,
             position='branch-right')
Exemple #3
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 def _add_header(self, 
                header_name,
                column_add=0):
     
     n = TextFace(f'{header_name}')
     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.
     # add header
     self.tss.aligned_header.add_face(n, self.column_count-1+column_add)
def traitTree(tree, traits, mapper, outDir, floatSwitch=0):
    ### Take dict of traits and [R,G,B]-returning function
    ### Draw a tree with the continuous trait painted on via a colormapping function

    def rgb2hex(r, g, b):
        hex = "#{:02x}{:02x}{:02x}".format(r, g, b)
        return hex

    for n in tree.traverse():
        if n.is_leaf():
            n.set_style(nstyle_L)
            # a manual way to set leaf labels
            #n.add_face(TextFace(str(n.name)), column=0, position="aligned")
        else:
            n.set_style(nstyle)
        #nd = TextFace(str(n.ND)) # label with node ID
        # make the face
        if round == 0:
            nd = TextFace(str(int(round(
                traits[n.ND]))))  # label with rounded continuous trait value
        else:
            nd = CircleFace(
                10, color=rgb2hex(*[int(val) for val in mapper(traits[n.ND])]))
            #nd = TextFace(str(round(traits[n.ND], floatSwitch)))  # label with rounded continuous trait value

        #nd.background.color = rgb2hex(*[int(val) for val in mapper(traits[n.ND], gamma=0.8, scaleMax=255)]) # setup for wl2RGB
        #nd.background.color = rgb2hex(*[int(val) for val in mapper(traits[n.ND])])  # setup for grayscale
        nd.background.color = None
        #nd.margin_right = 2
        #nd.margin_top = 1
        #nd.margin_left = 2
        #nd.margin_bottom = 1
        nd.border.width = None
        nd.hz_align = 2
        #nd.inner_border.width = 1
        # outline for the circle node
        #ol = CircleFace(11, color = "black")
        #ol.hz_align = 0
        #n.add_face(ol, column=0, position="float-behind") #float-behind
        n.add_face(nd, column=0, position="float")  #float
        # this is necessary for some reason to keep the tree from collapsing
        n.add_face(TextFace("       "), column=0, position="branch-bottom")

    outFile = outDir + "/cont_trait.pdf"
    tree.render(outFile, tree_style=tree_style)
    print >> sys.stderr, outFile
Exemple #5
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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
Exemple #6
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    def add_heatmap(self, 
                    taxon2value, 
                    header_name,
                    continuous_scale=False,
                    show_text=False):
        
        from metagenlab_libs.colors import get_continuous_scale
        
        self._add_header(header_name)
                
        if continuous_scale:
            color_scale = get_continuous_scale(taxon2value.values())
        
        for i, lf in enumerate(self.tree.iter_leaves()):
            
            if not lf.name in taxon2value:
                n = TextFace('')
            else:
                value = taxon2value[lf.name]

                if show_text:
                    n = TextFace('%s' % value)
                else:
                    n = TextFace('    ')

                n.margin_top = 2
                n.margin_right = 3
                n.margin_left = 3
                n.margin_bottom = 2
                n.hz_align = 1
                n.vt_align = 1
                n.border.width = 3
                n.border.color = "#ffffff"
                if continuous_scale:
                    n.background.color = rgb2hex(color_scale[0].to_rgba(float(value)))
                n.opacity = 1.
                i+=1

            if self.rotate:
                n.rotation = 270
            lf.add_face(n, self.column_count, position="aligned")
        
        self.column_count += 1
Exemple #7
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 def my_layout(node):
     circle_color = 'lightgray' if colormap is None or node.name not in colormap else colormap[
         node.name]
     text_color = 'black'
     if isinstance(circle_color, str):
         if isolabel and hasattr(node, 'isotype'):
             nl = ''.join(
                 sorted(set([ISO_SHORT[iss] for iss in node.isotype]),
                        key=lambda x: ISO_TYPE_charORDER[x]))
         else:
             nl = str(node.frequency)
         C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
                        color=circle_color,
                        label={
                            'text': nl,
                            'color': text_color
                        } if node.frequency > 0 else None)
         C.rotation = -90
         C.hz_align = 1
         faces.add_face_to_node(C, node, 0)
     else:
         P = PieChartFace(
             [100 * x / node.frequency for x in circle_color.values()],
             2 * 10 * scipy.sqrt(node.frequency),
             2 * 10 * scipy.sqrt(node.frequency),
             colors=[(color if color != 'None' else 'lightgray')
                     for color in list(circle_color.keys())],
             line_color=None)
         T = TextFace(' '.join(
             [str(x) for x in list(circle_color.values())]),
                      tight_text=True)
         T.hz_align = 1
         T.rotation = -90
         faces.add_face_to_node(P, node, 0, position='branch-right')
         faces.add_face_to_node(T, node, 1, position='branch-right')
     if idlabel:
         T = TextFace(node.name, tight_text=True, fsize=6)
         T.rotation = -90
         T.hz_align = 1
         faces.add_face_to_node(
             T,
             node,
             1 if isinstance(circle_color, str) else 2,
             position='branch-right')
     elif isolabel and hasattr(node, 'isotype') and False:
         iso_name = ''.join(
             sorted(set([ISO_SHORT[iss] for iss in node.isotype]),
                    key=lambda x: ISO_TYPE_charORDER[x]))
         #T = TextFace(iso_name, tight_text=True, fsize=6)
         #T.rotation = -90
         #T.hz_align = 1
         #faces.add_face_to_node(T, node, 1 if isinstance(circle_color, str) else 2, position='branch-right')
         C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
                        color=circle_color,
                        label={
                            'text': iso_name,
                            'color': text_color
                        } if node.frequency > 0 else None)
         C.rotation = -90
         C.hz_align = 1
         faces.add_face_to_node(C, node, 0)
Exemple #8
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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([item['ID'] for item in grp.COGs]) if len(grp.COGs)>0 else '', \
        str([item['ID'] for item in grp.NOGs]) if len(grp.NOGs)>0 else '', \
        str([item['ID'] for item in grp.PFAMs])] if len(grp.PFAMs)>0 else '')\
                    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)
Exemple #9
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def generateFigure(PF, sample, rank, input_file, output_base_name, file_type, plot_l1, scaling, output_dpi):

    # Make the ETE3 tree
    try:
        tree = ncbi.get_topology(PF.get_all_tax_ids(sample), rank_limit=rank)

    except:
        logging.getLogger('Tampa').critical("Input format not compatible.")
        exit(1)

    ts = TreeStyle()
    ts.layout_fn = PF.layout
    ts.mode = "c"
    ts.show_leaf_name = False
    ts.show_branch_length = False
    ts.show_branch_support = False
    ts.min_leaf_separation = 10
    ts.arc_span = 360
    #ts.legend.add_face(CircleFace(100, "#1b9e77", label="Predicted"), column=0)
    #ts.legend.add_face(CircleFace(100, '#d95f02', label="True"), column=1)
    # add white space to move the legend closer
    ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=2)
    ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=1)
    ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=0)
    ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=2)
    ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=1)
    ts.legend.add_face(CircleFace(65, "#FFFFFF"), column=0)

    # add the legend
    legend_fs = 50
    C1 = CircleFace(100, "#1b9e77")
    C1.hz_align = True
    ts.legend.add_face(C1, column=0)
    T1 = TextFace("Predicted", fsize=legend_fs)
    T1.hz_align = True
    ts.legend.add_face(T1, column=0)

    if len(PF.ground_truth_dict) > 0:
        C2 = CircleFace(100, "#d95f02")
        C2.hz_align = True
        ts.legend.add_face(C2, column=1)
        T2 = TextFace("True", fsize=legend_fs)
        T2.hz_align = True
        ts.legend.add_face(T2, column=1)

    T3 = TextFace(f"Tool: {os.path.basename(input_file).split('.')[0]}", fsize=legend_fs)
    T3.hz_align = True
    ts.legend.add_face(T3, column=0)
    ts.allow_face_overlap = False  # this lets me mess a bit with font size and face size without the interaction of the two
    ts.min_leaf_separation = 10
    tree_output_file = f"{output_base_name}_tree_{rank}_{sample}.{file_type}"
    tree.render(tree_output_file, h=5.2, w=5, tree_style=ts, units="in", dpi=output_dpi)


    if plot_l1:

        # if you asked for L1 too, then plot that
        true_abundance_at_rank = []
        predicted_abundance_at_rank = []
        for node in tree.get_leaves():
            if node.rank == rank:
                tax_id = str(node.taxid)
                if tax_id in PF.ground_truth_tax_id_to_percentage:
                    true_abundance_at_rank.append(PF.ground_truth_tax_id_to_percentage[str(node.taxid)] / 100.)
                else:
                    true_abundance_at_rank.append(0)
                if tax_id in PF.profile_tax_id_to_percentage:
                    predicted_abundance_at_rank.append(PF.profile_tax_id_to_percentage[str(node.taxid)] / 100.)
                else:
                    predicted_abundance_at_rank.append(0)

        data = np.zeros((len(true_abundance_at_rank), 2))
        data[:, 0] = np.array(true_abundance_at_rank)
        data[:, 1] = np.array(predicted_abundance_at_rank)

        df = pd.DataFrame(data, columns=['True', 'Predicted'])
        # g = seaborn.FacetGrid(df, height=6)
        ax = seaborn.scatterplot(x='True', y='Predicted', data=df, color='b', s=55)
        eps = 1
        ax.set_aspect('equal')
        max_val = np.max(data) + eps
        ax.set_xlim(-.5, max_val)
        ax.set_ylim(-.5, max_val)
        ax.set_xbound(-.5, max_val)
        ax.set_ybound(-.5, max_val)

        #plt.figure(figsize=(6,6))
        plt.plot(np.linspace(0, max_val, 100), np.linspace(0, max_val, 100), color='k')

        for (x, y) in zip(true_abundance_at_rank, predicted_abundance_at_rank):
            if x > y:
                ax.vlines(x, y, x, colors='r')
            if y > x:
                ax.vlines(x, x, y, colors='r')
        plt.title(f"Tool: {os.path.basename(input_file).split('.')[0]}")
        plt.tight_layout()
        l1_out_file = f"{output_base_name}_L1_{rank}.{file_type}"
        plt.savefig(l1_out_file, dpi=output_dpi)
Exemple #10
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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
Exemple #11
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def make_cluster_tree(tree_file: str,
                      matrix: str,
                      out_file: str,
                      outgroup: Optional[List[str]] = None) -> None:
    """Draw a tree with cluster absence/presence information from an existing
    tree file and absence/presence matrix, and save it as an image under the
    supplied file name.

    Arguments:
        tree_file: the name of the file containing the tree to annotate
        matrix:    a comma- or tab-separated absence/presence matrix
        out_file:  the name under which to save the resulting image
        outgroup:  the organism(s) to use as an outgroup, if any
    """
    # ClusterTree needs tab-separated, but that can't be exported cleanly
    matrix = matrix.replace(",", "\t")
    # tree with clustering analysis
    tree = ClusterTree(tree_file, text_array=matrix)

    # rerooting the tree
    if outgroup:
        ancestor = tree.get_common_ancestor(outgroup)
        tree.set_outgroup(ancestor)
        tree.ladderize(direction=1)

    # set drawing line width to 2
    my_node_style = NodeStyle()
    my_node_style["vt_line_width"] = 2
    my_node_style["hz_line_width"] = 2
    my_node_style["size"] = 5

    # layout function
    def sel_mylayout(node):
        node.set_style(my_node_style)

        if node.is_leaf():
            # add names in larger font + italics
            species_name = AttrFace("name", fsize=12, fstyle="italic")
            add_face_to_node(species_name,
                             node,
                             column=0,
                             position="branch-right")
            # add absence/presence matrix
            for i, value in enumerate(getattr(node, "profile", [])):
                if value > 0:
                    color = "#FF0000"
                else:
                    color = "#EEEEEE"
                my_face = CircleFace(8, color, style="circle")
                my_face.margin_right = 3
                my_face.margin_bottom = 3
                add_face_to_node(my_face, node, position="aligned", column=i)

    # Use my layout to visualize the tree
    my_tree_style = TreeStyle()

    # Add header
    for j, name in enumerate(tree.arraytable.colNames):
        name_face = TextFace(name, fsize=11)
        name_face.rotation = -90
        name_face.hz_align = 1
        name_face.vt_align = 1
        name_face.margin_bottom = 10
        my_tree_style.aligned_header.add_face(name_face, column=j)

    my_tree_style.scale_length = 0.1
    # myTreeStyle.show_branch_support = True
    # don't auto-show leaf names, since we dealt with that above
    my_tree_style.show_leaf_name = False

    # set layout function for my_tree_style
    my_tree_style.layout_fn = sel_mylayout

    #tree.render(out_file, w=183, units="mm", dpi=600, tree_style=my_tree_style)
    tree.render(out_file, dpi=600, tree_style=my_tree_style)
Exemple #12
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
def plot_ete_tree(tree_file,
                  ordered_queries,
                  leaf_id2protein_id2identity,
                  leaf_id2mlst,
                  leaf_id2spa,
                  leaf_id2meca,
                  show_identity_values=True,
                  leaf_id2description=False):
    mlst_list = list(set(leaf_id2mlst.values()))
    mlst2color = dict(zip(mlst_list, get_spaced_colors(len(mlst_list))))
    mlst2color['-'] = 'white'

    t1 = Tree(tree_file)
    tss = TreeStyle()
    R = t1.get_midpoint_outgroup()
    t1.set_outgroup(R)
    t1.ladderize()

    head = True
    column_add = 4
    for lf in t1.iter_leaves():
        lf.branch_vertical_margin = 0
        # add MLST
        if head:
            n = TextFace(' MLST ')
            n.margin_top = 2
            n.margin_right = 2
            n.margin_left = 2
            n.margin_bottom = 2
            n.rotation = 270
            n.vt_align = 2
            n.hz_align = 2
            n.inner_background.color = "white"
            n.opacity = 1.
            tss.aligned_header.add_face(n, 1)

        if lf.name in leaf2mlst:
            n = TextFace(' %s ' % leaf_id2mlst[lf.name])
            n.inner_background.color = 'white'
            m = TextFace('  ')
            m.inner_background.color = mlst2color[leaf_id2mlst[lf.name]]
        else:
            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 = 20
        m.margin_bottom = 2

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

        # add spa typing
        if head:
            n = TextFace(' spa ')
            n.margin_top = 2
            n.margin_right = 2
            n.margin_left = 2
            n.margin_bottom = 2
            n.rotation = 270
            n.vt_align = 2
            n.hz_align = 2
            n.inner_background.color = "white"
            n.opacity = 1.
            tss.aligned_header.add_face(n, column_add-2)
        if lf.name in leaf_id2spa:
            n = TextFace(' %s ' % leaf_id2spa[lf.name])
            n.inner_background.color = "white"
        else:
            n = TextFace('  na  ')
            n.inner_background.color = "grey"
        n.opacity = 1.
        n.margin_top = 2
        n.margin_right = 2
        n.margin_left = 2
        n.margin_bottom = 2

        lf.add_face(n, column_add-2, position="aligned")

        # add mecA typing
        if head:
            n = TextFace(' mecA ')
            n.margin_top = 2
            n.margin_right = 2
            n.margin_left = 2
            n.margin_bottom = 2
            n.rotation = 270
            n.vt_align = 2
            n.hz_align = 2
            n.inner_background.color = "white"
            n.opacity = 1.
            tss.aligned_header.add_face(n, column_add-1)
        if lf.name in leaf_id2meca:
            n = TextFace(' %s ' % leaf_id2meca[lf.name])
            if leaf_id2meca[lf.name] == 'Perfect':
                n.inner_background.color = "red"
            elif leaf_id2meca[lf.name] == 'Strict':
                n.inner_background.color = "orange"
            else:
                n.inner_background.color = "white"
        else:
            n = TextFace('   na   ')
            n.inner_background.color = "grey"
        n.opacity = 1.
        n.margin_top = 2
        n.margin_right = 2
        n.margin_left = 2
        n.margin_bottom = 2

        lf.add_face(n, column_add-1, position="aligned")

        # loop to add virulence gene hits
        for column, protein_id in enumerate(ordered_queries):
            # draw labels at the top of each column
            if head:
                if show_identity_values:
                    n = TextFace(' %s ' % str(protein_id))
                    n.margin_top = 2
                    n.margin_right = 2
                    n.margin_left = 2
                    n.margin_bottom = 2
                    n.rotation = 270
                    n.vt_align = 2
                    n.hz_align = 2
                    n.inner_background.color = "white"
                    n.opacity = 1.
                    tss.aligned_header.add_face(n, column+column_add)
                else:
                    n = TextFace(' %s ' % str(protein_id), fsize=6)
                    n.margin_top = 0
                    n.margin_right = 0
                    n.margin_left = 0
                    n.margin_bottom = 0
                    n.rotation = 270
                    n.vt_align = 2
                    n.hz_align = 2
                    n.inner_background.color = "white"
                    n.opacity = 1.
                    # lf.add_face(n, col, position="aligned")
                    tss.aligned_header.add_face(n, column+column_add)
            # draw column content
            if lf.name not in leaf_id2protein_id2identity:
                n = TextFace(' %s ' % str('  na  '))
                n.opacity = 1.
                n.margin_top = 2
                n.margin_right = 2
                n.margin_left = 2
                n.margin_bottom = 2
                n.inner_background.color = "grey"
                lf.add_face(n, column+column_add, position="aligned")
            else:
                if protein_id in leaf_id2protein_id2identity[lf.name]:
                    identity_value = float(leaf_id2protein_id2identity[lf.name][protein_id])
                    color = rgb2hex(m_blue.to_rgba(identity_value))


                    if show_identity_values:
                        # report identity values in coloured boxes
                        # adapt box size depending the digit width
                        if str(identity_value) == '100.00' or str(identity_value) == '100.0':
                            identity_value = '100'
                            n = TextFace(" %s  " % identity_value)
                        else:
                            n = TextFace("%.2f" % round(float(identity_value), 2))
                        # color text to white for dark cells
                        if float(identity_value) > 95:
                            n.fgcolor = "white"
                        n.opacity = 1.
                        n.margin_top = 2
                        n.margin_right = 2
                        n.margin_left = 2
                        n.margin_bottom = 2
                        n.inner_background.color = color
                        lf.add_face(n, column+column_add, position="aligned")
                    else:
                        # draw coloured boxes without text
                        n = TextFace('  ')
                        n.margin_top = 0
                        n.margin_right = 0
                        n.margin_left = 0
                        n.margin_bottom = 0
                        # n.color = color
                        n.inner_background.color = color
                        lf.add_face(n, column+column_add, position="aligned")
                else:
                    n = TextFace('  %s  ' % str('  -  '))
                    n.opacity = 1.
                    n.margin_top = 2
                    n.margin_right = 2
                    n.margin_left = 2
                    n.margin_bottom = 2
                    n.inner_background.color = "white"
                    lf.add_face(n, column+column_add, position="aligned")

        # end of first leaf: turn off header
        head = False

    # add boostrap supports
    for n in t1.traverse():
        nstyle = NodeStyle()
        if n.support < 0.9:
            nstyle["fgcolor"] = "blue"
            nstyle["size"] = 6
            n.set_style(nstyle)
        else:
            nstyle["fgcolor"] = "red"
            nstyle["size"] = 0
            n.set_style(nstyle)

    return t1, tss
    def custom_layout(self,node):
        if node.is_leaf():
           aligned_name_face = TextFace(node.name, fgcolor='olive', fsize=12)
           aligned_name_face.margin_top = 5
           aligned_name_face.margin_right = 5
           aligned_name_face.margin_left = 5
           aligned_name_face.margin_bottom = 5
           aligned_name_face.hz_align = 0     #0 = left, 1 = center, 2 = right 
           add_face_to_node(aligned_name_face, node, column=2, position='aligned')
           #name_face = TextFace(node.name, fgcolor='#333333', fsize=11)
           #name_face.margin_top = 3
           #name_face.margin_right = 3
           #name_face.margin_left = 3
           #name_face.margin_bottom = 3 
           #add_face_to_node(name_face, node, column=2, position='branch-right')
           node.img_style['size'] = 0
           #---------------------------------------------
           #displaying extra categorical and numeric data
           if (node.name in self._tip2info):
              column_no = 3
              for headerIndex, dataheader in enumerate(self._tip2headers):
                  extra_data = self._tip2info[node.name][headerIndex]
                  if isinstance( extra_data, ( int, float ) ):
                     extra_face = BarChartFace([extra_data], width=100,height=25,colors=[self._tip2color[node.name][headerIndex]],labels=[dataheader],min_value=0.0,max_value=self._tip_max)
                  else:
                     extra_face = TextFace(extra_data, fsize=11, fgcolor='black')
                     extra_face.background.color = self._tip2color[node.name][headerIndex]

                  extra_face.margin_left = 5
                  extra_face.margin_top = 5
                  extra_face.margin_right = 5
                  extra_face.margin_bottom = 5
                   
                  add_face_to_node(extra_face, node, column=column_no, position='aligned')
                  #add_face_to_node(extra_face, node, column=column_no, aligned = True, position='branch-right')
                  column_no += 1
           else:
              #print "No data available"
              column_no = 3
              for headerIndex, dataheader in enumerate(self._tip2headers):     
                  extra_face = TextFace("No data available", fsize=10, fgcolor='black')
         
                  extra_face.margin_left = 5
                  extra_face.margin_top = 5
                  extra_face.margin_right = 5
                  extra_face.margin_bottom = 5
              
                  add_face_to_node(extra_face, node, column=column_no, position='aligned')
                  column_no += 1

           image_col_no = column_no
           #----------------------------------------------
           if (node.name in self._img_chk_list):
              if self._img_data_dic[node.name] is not None:
                  img_face = ImgFace(self._img_data_dic[node.name], is_url=True)
                  #img_face = ImgFace(self._tip2info[node.name][0], is_url=True)
                  #img_path = os.path.join("file:///home/tayeen/TayeenFolders/TreeViewer/WebTreeApp/newplugin_test/data/", "328653.jpg")
                  #img_face = ImgFace(img_path, is_url=True)
                  img_face.margin_top = 10
                  img_face.margin_right = 10
                  img_face.margin_left = 10
                  img_face.margin_bottom = 10
                  #add_face_to_node(img_face, node, column=3, position='branch-right')
                  #add_face_to_node(img_face, node, column=3, aligned= True, position='branch-right')
              else:
                  img_path = os.path.join("file://"+image_path, "ina.jpg")
                  img_face = ImgFace(img_path, is_url=True)  
              
              #add_face_to_node(img_face, node, column=5, position='branch-right')
              add_face_to_node(img_face, node, column=image_col_no, position='aligned')
                   
        else: #node is not a leaf
            node.img_style['size'] = 4
            node.img_style['shape'] = 'square'
        
            if node.name and self._custom_options["draw_internal"]:
              name_face = TextFace(node.name, fgcolor='grey', fsize=10)
              name_face.margin_top = 4
              name_face.margin_right = 4
              name_face.margin_left = 4
              name_face.margin_bottom = 4
              add_face_to_node(name_face, node, column=0, position='branch-top')
            
            if node.name in self._node2label: 
               label_face = TextFace(self._node2label[node.name], fgcolor='DarkGreen', fsize=10)
               label_face.margin_top = 4
               label_face.margin_right = 4
               label_face.margin_left = 4
               label_face.margin_bottom = 4
               add_face_to_node(label_face, node, column=0, position="branch-top")
            
            if node.support and self._custom_options["draw_support"]:
              support_face = TextFace(node.support, fgcolor='indianred', fsize=10)
              support_face.margin_top = 4
              support_face.margin_right = 4
              support_face.margin_left = 4
              support_face.margin_bottom = 4
              add_face_to_node(support_face, node, column=0, position='branch-bottom')
              
              

            if hasattr(node, "hide") and int(node.hide) == 1:
              node.img_style["draw_descendants"]= False
              collapsed_face = faces.TextFace(" %s collapsed leaves." %len(node), \
                    fsize=10, fgcolor="#444", ftype="Arial")
              faces.add_face_to_node(collapsed_face, node, 0)
            else:
              node.img_style["draw_descendants"] = True

            # Parse node features features and conver them into styles. This must be done like this, since current ete version 
            #does not allow modifying style outside the layout function.
            if hasattr(node, "bsize"):
              node.img_style["size"]= int(node.bsize)

            if hasattr(node, "shape"):
              node.img_style["shape"]= node.shape

            if hasattr(node, "bgcolor"):
              node.img_style["bgcolor"]= node.bgcolor

            if hasattr(node, "fgcolor"):
              node.img_style["fgcolor"]= node.fgcolor
        #parse all nodes features
        
        if hasattr(node, "bh_bgcolor"):
           node.img_style["bgcolor"]= node.bh_bgcolor
        if hasattr(node, "bh_size"):
           node.img_style["size"]= node.bh_size
       
        if hasattr(node, "lh_color"):
           node.img_style['hz_line_color'] = node.lh_color
           node.img_style["vt_line_color"] = node.lh_color
        
        if hasattr(node, "lh_width"):
           node.img_style['hz_line_width'] = node.lh_width
           node.img_style['vt_line_width'] = node.lh_width

        if hasattr(node, "lh_width") and hasattr(node, "lh_color"):
           for n in node.iter_descendants():
               n.img_style['hz_line_color'] = node.lh_color
               n.img_style["vt_line_color"] = node.lh_color
               n.img_style['hz_line_width'] = node.lh_width
               n.img_style['vt_line_width'] = node.lh_width
Exemple #15
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
Exemple #16
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
Exemple #17
0
def plot_heat_tree_V1(taxid2n,
                      tree_file,
                      genes,
                      taxid2st=False,
                      leaf_label_conversion_dico=False):
    '''
    Plot heatmap next to a tree. The order of the heatmap **MUST** be the same,
    as order of the leafs on the tree. The tree must be in the Newick format. If
    *output_file* is specified, then heat-tree will be rendered as a PNG,
    otherwise interactive browser will pop-up with your heat-tree.

    TODO ajouter en option la possibilite d'ajouter en option la valeur dans la cellule

    Parameters
    ----------


    tree_file: str
        Path to the tree file in Newick format. The leaf node labels should
        be the same as as row names in the heatmap file. E.g. row1, row2.

    output_file: str, optional
        If specified the heat-tree will be rendered in that file as a PNG image,
        otherwise interactive browser will pop-up. **N.B.** program will wait
        for you to exit the browser before continuing.
    '''

    t1 = Tree(tree_file)
    tss = TreeStyle()
    #t.populate(8)
    # Calculate the midpoint node
    R = t1.get_midpoint_outgroup()
    # and set it as tree outgroup
    t1.set_outgroup(R)  # To operate with numbers efficiently

    import matplotlib.cm as cm
    from matplotlib.colors import rgb2hex
    import matplotlib as mpl
    norm = mpl.colors.Normalize(vmin=0.8, vmax=1)  # map2count[map[0]][0]
    cmap_blue = cm.Blues
    m2 = cm.ScalarMappable(norm=norm, cmap=cmap_blue)

    leaf_number = 0
    for lf in t1.iter_leaves():
        leaf_number += 1
        lf.branch_vertical_margin = 0

        try:
            data = taxid2n[str(lf.name)]
        except:
            data = [0]

        try:
            st = taxid2st[lf.name]
        except:
            st = False
            '''
            if "taxon2accession_list" not in locals():
                from chlamdb.biosqldb import manipulate_biosqldb
                server, db = manipulate_biosqldb.load_db("k_cosson_05_16")
                sql = 'select taxon_id, accession from bioentry where biodatabase_id=104'
                data_tax = server.adaptor.execute_and_fetchall(sql,)
                taxon2accession_list = {}
                for i in data_tax:
                    if i[0] not in taxon2accession_list:
                        taxon2accession_list[i[0]] = [i[1]]
                    else:
                       taxon2accession_list[i[0]].append(i[1])
            else:
                for taxon in taxon2accession_list:
                    if lf.name in taxon2accession_list[taxon]:
                        for accession in taxon2accession_list[taxon]:
                            print lf.name, accession
                            try:
                                st = taxid2st[accession]
                                data = taxid2n[accession]
                                print 'st ok!!', st
                                break
                            except:
                                continue
             '''

        if accession2description:
            try:
                lf.name = accession2description[lf.name]
            except:
                pass
        if st:
            lf.name = lf.name + ' (' + st + ')'
        else:
            pass
        for col, value in enumerate(data):

            if leaf_number == 1:
                n = TextFace('%s' % (genes[col]), fsize=6)
                n.vt_align = 2
                n.hz_align = 2
                n.rotation = 270
                n.margin_top = 0
                n.margin_right = 0
                n.margin_left = 4
                n.margin_bottom = 0
                n.inner_background.color = "white"
                n.opacity = 1.
                tss.aligned_header.add_face(n, col)
                #lf.add_face(n, col, position="aligned")

            if value > 0:
                n = TextFace('  ')
                n.margin_top = 0
                n.margin_right = 0
                n.margin_left = 0
                n.margin_bottom = 0
                n.inner_background.color = rgb2hex(m2.to_rgba(
                    float(value)))  #'#140718' #"#81BEF7"
                n.opacity = 1.
                lf.add_face(n, col, position="aligned")

            else:
                n = TextFace('  ')
                n.margin_top = 0
                n.margin_right = 0
                n.margin_left = 0
                n.margin_bottom = 0
                n.inner_background.color = "white"
                n.opacity = 1.
                lf.add_face(n, col, position="aligned")

    return t1, leaf_number, tss
Exemple #18
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
Exemple #19
0
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)