コード例 #1
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ファイル: etefmt.py プロジェクト: pythseq/phylonium
def layout(node):
	if node.is_leaf(): 
		pretty_name = names[node.name] if node.name in names else node.name
		# derp = AttrFace("name", fsize=10, ftype="Arial", fgcolor="black")
		pretty_name_face = faces.TextFace(pretty_name)
		pretty_name_face.margin_left = 5
		faces.add_face_to_node(pretty_name_face, node, column=0)
コード例 #2
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def layout(node):
    ##    if node.is_leaf() and 'showname' in node.features:
    ##        # Add node name to laef nodes
    ##        N = AttrFace("name", fsize=14, fgcolor="black")
    ##        faces.add_face_to_node(N, node, 0)
    if "Rsize" in node.features:
        # Creates a sphere face whose size is proportional to node's
        # feature "Rsize"
        C = CircleFace(radius=node.Rsize * 3,
                       color="RoyalBlue",
                       style="sphere")
        # make the sphere transparent
        C.opacity = 0.9
        # And place as a float face over the tree
        faces.add_face_to_node(C, node, 0, position="float")
    if "Rpearsize" in node.features:
        # Creates a sphere face whose size is proportional to node's
        # feature "Rpearsize"
        C = CircleFace(radius=node.Rpearsize * 3,
                       color="lightgreen",
                       style="sphere")
        # make the sphere transparent
        C.opacity = 0.9
        # And place as a float face over the tree
        faces.add_face_to_node(C, node, 0, position="float")
コード例 #3
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def mylayout(node):
    # Internal Node formatting
    nstyle = NodeStyle()
    nstyle["size"] = 0
    nstyle["vt_line_width"] = 2
    nstyle["hz_line_width"] = 2

    if node.is_leaf():
        circle_face = CircleFace(10, color_dict[node.name], style='circle')
        faces.add_face_to_node(circle_face,
                               node,
                               position="branch-right",
                               column=0)

        text_face = TextFace(meta_dict[node.name][0])
        text_face.fgcolor = color_dict[node.name]
        faces.add_face_to_node(text_face,
                               node,
                               position="branch-right",
                               column=1)

        node.set_style(nstyle)

    elif node.is_root():
        node.dist = 0
        node.set_style(nstyle)

    else:
        node.set_style(nstyle)
コード例 #4
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    def my_layout(node):
        N = None
        # If user specified labels are specified add these:
        if 'node_label' in tree_features:
            for t in tree_features['node_label']:
                node_attr = ifhasthenget(node, t)
                if node_attr and to_string(node_attr):
                    if t == 'name' and hasattr(node, 'cl'):
                        continue
                    textface = to_string(node_attr)
                    N = TextFace(textface, fsize=12, fgcolor='black')
                    if 'e-' in textface and to_float(
                            textface
                    ):  # Stupid exception because ete3 rendering doesn't understand scientific notation
                        N = TextFace('%2.1e    ' % to_float(textface),
                                     fsize=12,
                                     fgcolor='black')

        # Add default values:
        elif not no_default and node.frequency > 1 and not hasattr(node, 'cl'):
            N = TextFace(
                node.frequency, fsize=12,
                fgcolor='black')  # Default: use node frequency as TextFace

        if N is not None:
            N.rotation = -90
            faces.add_face_to_node(N, node, 0, position='branch-top')
コード例 #5
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def layout(node):
    """
    Helper function to annotate nodes with scientific name
    :param node: A node instance of a ete3.Tree
    :return: Annotated node with sci_name
    """
    faces.add_face_to_node(TextFace(node.sci_name), node, 0)
コード例 #6
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    def my_layout(node):

        style = NodeStyle()
        style["size"] = 0
        style["vt_line_color"] = "#A0A0A0"
        style["hz_line_color"] = "#A0A0A0"
        style["vt_line_type"] = 0  # 0 solid, 1 dashed, 2 dotted
        style["hz_line_type"] = 0
        node.set_style(style)

        if node.is_leaf():
            name_face = AttrFace("name", fsize=8, ftype="Times")
        else:
            name_face = TextFace(node.name, fsize=18, ftype="Times")
            if node.node_type == Sum:
                for child in node.children:
                    label = TextFace(round(child.support, 3), fsize=6)
                    child.add_face(label, column=1, position="branch-bottom")
        if show_ids:
            node.add_face(AttrFace("id", fsize=6),
                          column=1,
                          position="branch-top")
        faces.add_face_to_node(name_face,
                               node,
                               column=1,
                               position="branch-right")
コード例 #7
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 def treeLayout(self, node):
     if node.is_leaf():
         faces.add_face_to_node(AttrFace("name"), node, column=0)
     else:
         node.img_style["size"] = 4
         node.img_style["shape"] = "sphere"
         node.img_style["fgcolor"] = "#AA0000"
コード例 #8
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ファイル: balances.py プロジェクト: mortonjt/canvas
def barchart_layout(node, name='name',
                    width=20, height=40,
                    colors=None, min_value=0, max_value=1,
                    fsize=14, fgcolor="black"):
    if colors is None:
        colors = ['#0000FF']
    if node.is_leaf():
        # Add node name to leaf nodes
        N = AttrFace("name", fsize=fsize, fgcolor=fgcolor)

        faces.add_face_to_node(N, node, 0)
    if "weight" in node.features:
        # Creates a sphere face whose size is proportional to node's
        # feature "weight"
        if (isinstance(node.weight, int) or isinstance(node.weight, float)):
            weight = [node.weight]
        else:
            weight = node.weight
        C = BarChartFace(values=weight, width=width, height=height,
                         colors=['#0000FF'], min_value=min_value,
                         max_value=max_value)
        # Let's make the sphere transparent
        C.opacity = 0.5
        # Rotate the faces by 270*
        C.rotation = 270
        # And place as a float face over the tree
        faces.add_face_to_node(C, node, 0, position="float")
コード例 #9
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ファイル: names.py プロジェクト: anhelinaosiieva/Project
def mylayout(node):

    if node.is_leaf():
        longNameFace = faces.TextFace(code_name[node.name],
                                      fsize=15,
                                      fgcolor="green")
        faces.add_face_to_node(longNameFace, node, column=0)
コード例 #10
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ファイル: tree.py プロジェクト: ballardt/mti
def tree_layout(node):
    """
    TODO
    """
    if node.is_leaf():
        nameSize = 14
        nameColor = '#009000'
        relAbundSize = 10
    else:
        nameSize = 10
        nameColor = '#303030'
        relAbundSize = 8

    nameFace = faces.TextFace(node.name, fsize=nameSize, fgcolor=nameColor)
    nameFace.margin_bottom = 5
    nameFace.margin_right = 10
    nameFace.margin_left = 5
    faces.add_face_to_node(nameFace, node, column=0, position='branch-top')

    relAbundFace = faces.TextFace(node.rel_abund,
                                  fsize=relAbundSize,
                                  fgcolor='#2148c8')
    relAbundFace.margin_top = 5
    relAbundFace.margin_left = 5
    faces.add_face_to_node(relAbundFace,
                           node,
                           column=0,
                           position='branch-bottom')
コード例 #11
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ファイル: item_faces.py プロジェクト: AlishaMechtley/ete
def master_ly(node):
    if node.is_leaf():
        # Create an ItemFAce. First argument must be the pointer to
        # the constructor function that returns a QGraphicsItem. It
        # will be used to draw the Face. Next arguments are arbitrary,
        # and they will be forwarded to the constructor Face function.
        F = faces.DynamicItemFace(ugly_name_face, 100, 50)
        faces.add_face_to_node(F, node, 0, position="aligned")
コード例 #12
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def layout(node):
    if node.is_leaf():
        N = AttrFace("name", fsize=10, fgcolor="black")
        faces.add_face_to_node(N, node, 0)
    if "weight" in node.features:
        C = CircleFace(radius=node.weight, color="blue", style="sphere")
        C.opacity = 0.3
        faces.add_face_to_node(C, node, 0, position="float")
コード例 #13
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ファイル: item_faces.py プロジェクト: muppetjones/ete
def master_ly(node):
    if node.is_leaf():
        # Create an ItemFAce. First argument must be the pointer to
        # the constructor function that returns a QGraphicsItem. It
        # will be used to draw the Face. Next arguments are arbitrary,
        # and they will be forwarded to the constructor Face function.
        F = faces.DynamicItemFace(ugly_name_face, 100, 50)
        faces.add_face_to_node(F, node, 0, position="aligned")
コード例 #14
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def layout(node):
    if not node.is_leaf():
        size = random.randint(20,50)
        F= faces.PieChartFace([10,20,60,10],
                              colors=COLOR_SCHEMES[random.sample(schema_names, 1)[0]],
                              width=size, height=size)
        F.border.width = None
        F.opacity = 0.6
        faces.add_face_to_node(F,node, 0, position="float")
コード例 #15
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 def mylayout(node):
     #if node.name != 'L':
     file = 'tmp/%s.png' % node.name
     new_face = faces.ImgFace(file)
     new_face.rotable = True
     new_face.rotation = -90
     #new_face.margin_top = 50
     new_face.margin_left = 15
     faces.add_face_to_node(new_face, node, column=0 , position='branch-top')
コード例 #16
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ファイル: layouts.py プロジェクト: josenavas/gneiss
def barchart_layout(node, name='name',
                    width=20, height=40,
                    colors=None, min_value=0, max_value=1,
                    fsize=14, fgcolor="black",
                    alpha=0.5,
                    rotation=270):
    """
    Specifies the layout for the ete.TreeStyle object.

    Parameters
    ----------
    node: ete.Tree
        Input node for specifying which attributes.
    name: str, optional
        Attribute to look up the name of the node.
    width: int, optional
        Width of the barchart.
    height: int, optional
        Height of the barchart.
    colors: list of str, optional
        List of HTML colors to color the barchart values.
    min_value: int, optional
        Minimum value to set the scale of the chart.
    max_value: int, optional
        Maximum value to set the scale of the chart.
    fsize: int, optional
        Font size on the leafs.
    fgcolor: str, optional
        Font color of the leafs.
    alpha: float, optional
        Transparency of the barchart.
    rotation: int, optional
        Orientation of the barchart.
    """
    if colors is None:
        colors = ['#0000FF']
    if node.is_leaf():
        # Add node name to leaf nodes
        N = AttrFace("name", fsize=fsize, fgcolor=fgcolor)
        faces.add_face_to_node(N, node, 0)
    if "weight" in node.features:
        # Creates a sphere face whose size is proportional to node's
        # feature "weight"
        if (isinstance(node.weight, int) or isinstance(node.weight, float)):
            weight = [node.weight]
        else:
            weight = node.weight
        C = BarChartFace(values=weight, width=width, height=height,
                         colors=colors, min_value=min_value,
                         max_value=max_value)
        # Let's make the sphere transparent
        C.opacity = alpha
        # Rotate the faces by 270*
        C.rotation = rotation
        # And place as a float face over the tree
        faces.add_face_to_node(C, node, 0, position="float")
コード例 #17
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ファイル: plot.py プロジェクト: simonvh/gimmemotifs
def _tree_layout(node):
    try:
        from ete3 import AttrFace, faces
    except ImportError:
        print("Please install ete3 to use this functionality")
        sys.exit(1)

    if node.is_leaf():
        nameFace = AttrFace("name", fsize=24, ftype="Nimbus Sans L")
        faces.add_face_to_node(nameFace, node, 10, position="branch-right")
コード例 #18
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ファイル: draw_represent.py プロジェクト: MitsukiUsui/denovo
def layout(node):
    global represent_lst

    if node.is_leaf():
        N = AttrFace("name", fsize=14, fgcolor="black") #  can be "sci_name"
        faces.add_face_to_node(N, node, 0)
        
        if node.name in represent_lst:
            C = CircleFace(radius=5, color="black", style="sphere")
            faces.add_face_to_node(C, node, 1, position="aligned")
コード例 #19
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def tree_layout(node):
    """
    side function for tree layouts (following ete3 manual)
    :param node:
    :return:
    """
    if node.is_leaf():
        color = get_color(node.name)
        N = ete3.faces.TextFace(node.name, fsize=10, fgcolor=color)
        faces.add_face_to_node(N, node, 0)
コード例 #20
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def layout(node):
    if node.is_leaf():
        longNameFace = faces.TextFace(code_name[node.name],
                                      fsize=15,
                                      fgcolor="green")
        faces.add_face_to_node(longNameFace, node, column=0)
    if "weight" in node.features:
        C = CircleFace(radius=node.weight, color="blue", style="sphere")
        C.opacity = 0.3
        faces.add_face_to_node(C, node, 0, position="float")
コード例 #21
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def _tree_layout(node):
    try:
        from ete3 import AttrFace, faces
    except ImportError:
        print("Please install ete3 to use this functionality")
        sys.exit(1)

    if node.is_leaf():
        nameFace = AttrFace("name", fsize=24, ftype="Nimbus Sans L")
        faces.add_face_to_node(nameFace, node, 10, position="branch-right")
コード例 #22
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def layout(node):
    #print(node)
    if (len(node.get_ancestors()) < 4):
        print(node.name)
        n = AttrFace("name", fsize=9)
        n.margin_top = 10
        n.margin_bottom = 0
        n.margin_left = 10
        faces.add_face_to_node(n, node, 0, position="float")
        tf = TextFace(len(node.get_leaves()), fsize=12)
        faces.add_face_to_node(tf, node, 0, position="float")
コード例 #23
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def layout(node):
    if not node.is_leaf():
        size = random.randint(20, 50)
        F = faces.PieChartFace([10, 20, 60, 10],
                               colors=COLOR_SCHEMES[random.sample(
                                   schema_names, 1)[0]],
                               width=size,
                               height=size)
        F.border.width = None
        F.opacity = 0.6
        faces.add_face_to_node(F, node, 0, position="float")
コード例 #24
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def layout(node):
    # if node.is_leaf():
    #     # Add node name to leaf nodes
    #     N = AttrFace("name", fsize=14, fgcolor="black")
    #     faces.add_face_to_node(N, node, 0)
    if "weight" in node.features:
        # Creates a sphere face whose size is proportional to node's
        # feature "weight"
        C = CircleFace(radius=node.weight, color="RoyalBlue", style="sphere")
        # Let's make the sphere transparent
        C.opacity = 0.6
        # And place as a float face over the tree
        faces.add_face_to_node(C, node, 0, position="float")
コード例 #25
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ファイル: new_seq_face.py プロジェクト: AlishaMechtley/ete
def test_layout_phylo_nt(node):
    '''
    layout for CodemlTree
    '''
    if hasattr(node, "collapsed"):
        if node.collapsed == 1:
            node.img_style["draw_descendants"]= False
    if node.is_leaf():
        if hasattr (node, "sequence"):
            seqface =  MySequenceFace(node.sequence, "nt",
                                      fsize=10,
                                      col_w=11, interactive=True)
            faces.add_face_to_node(seqface, node, 1, aligned=True)
コード例 #26
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def layout(node):
    if node.is_leaf():
        # Add node name to laef nodes
        N = AttrFace("name", fsize=14, fgcolor="black")
        faces.add_face_to_node(N, node, 0)
    if "weight" in node.features:
        # Creates a sphere face whose size is proportional to node's
        # feature "weight"
        C = CircleFace(radius=node.weight, color="RoyalBlue", style="sphere")
        # Let's make the sphere transparent
        C.opacity = 0.3
        # And place as a float face over the tree
        faces.add_face_to_node(C, node, 0, position="float")
コード例 #27
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def mylayout(node):
    # If node is a leaf
    if node.is_leaf():
        # And a line profile
        faces.add_face_to_node(profileFace, node, 0, aligned=True)
        node.img_style["size"] = 0
        faces.add_face_to_node(nameFace, node, 1, aligned=True)

    # If node is internal
    else:
        # If silhouette is good, creates a green bubble
        if node.silhouette > 0:
            validationFace = faces.TextFace("Silh=%0.2f" % node.silhouette,
                                            "Verdana", 10, "#056600")
            node.img_style["fgcolor"] = "#056600"
        # Otherwise, use red bubbles
        else:
            validationFace = faces.TextFace("Silh=%0.2f" % node.silhouette,
                                            "Verdana", 10, "#940000")
            node.img_style["fgcolor"] = "#940000"

        # Sets node size proportional to the silhouette value.
        node.img_style["shape"] = "sphere"
        if node.silhouette <= 1 and node.silhouette >= -1:
            node.img_style["size"] = 15 + int((abs(node.silhouette) * 10)**2)

        # If node is very internal, draw also a bar diagram
        # with the average expression of the partition
        faces.add_face_to_node(validationFace, node, 0)
        if len(node) > 100:
            faces.add_face_to_node(cbarsFace, node, 1)
コード例 #28
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def layout(node):
    if node.is_leaf():
        if node.name=="A":
            node.color="Blue"
            node.attr2="Green"
        elif node.name=="B":
            node.color="Red"
            node.attr2="Orange"
        else:
            node.color="Grey"
            node.attr2="Yellow"
            
        faces.add_face_to_node( CircleFace(radius=5, color=node.color), node, column=1)
        faces.add_face_to_node( RectFace(width=10, height=10, fgcolor=node.attr2, bgcolor=node.attr2),   node, column=2)
コード例 #29
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def phyparts_pie_layout(mynode):
    if mynode.name in phyparts_pies:
        pie = faces.PieChartFace(
            phyparts_pies[mynode.name],
            #colors=COLOR_SCHEMES["set1"],
            colors=["blue", "green", "red", "dark gray"],
            width=50,
            height=50)
        pie.border.width = None
        pie.opacity = 0.5
        faces.add_face_to_node(pie, mynode, 0, position="branch-right")

        concord_text = faces.TextFace(str(int(concord_dict[mynode.name])) +
                                      '   ',
                                      fsize=20)
        conflict_text = faces.TextFace(str(int(conflict_dict[mynode.name])) +
                                       '   ',
                                       fsize=20)

        faces.add_face_to_node(concord_text, mynode, 0, position="branch-top")
        faces.add_face_to_node(conflict_text,
                               mynode,
                               0,
                               position="branch-bottom")

    else:
        F = faces.TextFace(mynode.name, fsize=20)
        faces.add_face_to_node(F, mynode, 0, position="aligned")
コード例 #30
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ファイル: tree_faces.py プロジェクト: AlishaMechtley/ete
def layout(node):
    if node.is_leaf():
        # Add node name to laef nodes
        N = AttrFace("name", fsize=14, fgcolor="black")
        faces.add_face_to_node(N, node, 0)

        t = Tree()
        t.populate(10)

        T = TreeFace(t, small_ts)
        # Let's make the sphere transparent
        T.opacity = 0.8
        # And place as a float face over the tree
        faces.add_face_to_node(T, node, 1, position="aligned")
コード例 #31
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ファイル: treeInTree.py プロジェクト: trung-hn/covid-19
def layout(node):
    if node.is_leaf():
        # Add node name to laef nodes
        N = AttrFace("name", fsize=14, fgcolor="black")
        faces.add_face_to_node(N, node, 0)

        t = Tree(tree)
        t.populate(10)

        T = TreeFace(t, small_ts)
        # Let's make the sphere transparent
        T.opacity = 0.8
        # And place as a float face over the tree
        faces.add_face_to_node(T, node, 1, position="aligned")
コード例 #32
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def my_layout(node):
    """Customise the layout of a tree node

    Args:
        node (node): tree node
    """
    if node.is_leaf():
        # If terminal node, draws its name
        name_face = AttrFace("name")
    else:
        # If internal node, draws label with smaller font size
        name_face = AttrFace("name", fsize=10)
    # Adds the name face to the image at the preferred position
    faces.add_face_to_node(name_face, node, column=0, position="branch-right")
コード例 #33
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ファイル: new_seq_face.py プロジェクト: muppetjones/ete
def test_layout_phylo_nt(node):
    '''
    layout for CodemlTree
    '''
    if hasattr(node, "collapsed"):
        if node.collapsed == 1:
            node.img_style["draw_descendants"] = False
    if node.is_leaf():
        if hasattr(node, "sequence"):
            seqface = MySequenceFace(node.sequence,
                                     "nt",
                                     fsize=10,
                                     col_w=11,
                                     interactive=True)
            faces.add_face_to_node(seqface, node, 1, aligned=True)
コード例 #34
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def layout(node):
    if node.is_leaf():
        if "Russia/" in node.name:
            Rudesc = faces.AttrFace("name", fsize=10)
            Rudesc.margin_left = 25
            faces.add_face_to_node(Rudesc, node, 0, aligned=True)
        else:
            if "_" in node.name:
                node.name = node.name.replace("_", " ")
            countrydesc = faces.AttrFace("name", fsize=10)
            countrydesc.margin_left = 5
            countrydesc.margin_bottom = 10
            countrydesc.margin_top = 5
            countrydesc.margin_right = 5
            faces.add_face_to_node(countrydesc, node, 0, aligned=False)
コード例 #35
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ファイル: new_seq_face.py プロジェクト: AlishaMechtley/ete
def test_layout_phylo_aa_motif(node):
    '''
    layout for CodemlTree
    '''
    if hasattr(node, "collapsed"):
        if node.collapsed == 1:
            node.img_style["draw_descendants"]= False
    special_col = [[10,100],[150,1000],[1000,2000],[3000,4990]]
    if node.is_leaf():
        if hasattr (node, "sequence"):
            seqface =  MySequenceFace(node.sequence, "aa",
                                      fsize=10,special_col=special_col,
                                      alt_col_w=3,
                                      col_w=11, interactive=True)
            faces.add_face_to_node(seqface, node, 1, aligned=True)
コード例 #36
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def layout_idtree(node):

    nstyle = NodeStyle()
    nstyle["size"] = 1
    node.set_style(nstyle)
    if node.is_leaf():
        # Add node name to leaf nodes
        N = AttrFace("name", fsize=14, fgcolor="black")
        faces.add_face_to_node(N, node, 0, position='aligned')

    if not node.is_root():
        # Creates a sphere face whose size is proportional to node's
        # feature "weight"

        TN = TextFace(str(node.ID), fsize=12)
        faces.add_face_to_node(TN, node, 1, position="branch-right")
コード例 #37
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def my_layout(node):
    if node.is_leaf():
        # If terminal node, draws its name
        name_face = AttrFace("name", ftype="Roboto", fgcolor='#191919')
        name_face.margin_right = 10
        name_face.margin_left = 10
    else:
        # If internal node, draws label with smaller font size
        name_face = AttrFace("name",
                             fsize=10,
                             ftype="Roboto",
                             fgcolor='#191919')
        name_face.margin_right = 10
        name_face.margin_left = 10
    # Adds the name face to the image at the preferred position
    faces.add_face_to_node(name_face, node, column=0, position="branch-right")
コード例 #38
0
def mylayout(node):
    if node.is_leaf():
        #        faces.add_face_to_node(nameFace, node, column=0)
        node.img_style["size"] = 80
        node.img_style["shape"] = "sphere"
        node.img_style["fgcolor"] = "#000000"
        L = node.name.split(' ')
        if len(L) > 1:
            img_name = os.path.join(g_suncg_object_path, L[1], "rgb_img",
                                    "8_rotation.png")
            objectFace = faces.ImgFace(img_name)
            faces.add_face_to_node(objectFace, node, column=0)
    else:
        node.img_style["size"] = 80
        node.img_style["shape"] = "sphere"
        node.img_style["fgcolor"] = "#AA0000"
コード例 #39
0
def layout(node):
    # If node is a leaf, add the nodes name and a its scientific name
    if node.is_leaf():
        F = faces.DynamicItemFace(scientific_name_face)
        if F.node == "DAR34208_Raffaelea_kilii_sp._nov.":
            F.background = "Black"
            faces.add_face_to_node(
                F,
                node,
                0,
            )
        F.margin_left = 10
        faces.add_face_to_node(
            F,
            node,
            0,
        )
コード例 #40
0
ファイル: random_draw.py プロジェクト: AlishaMechtley/ete
def aligned_faces(node):
    if node.is_leaf():
        for i in xrange(3):
            F = faces.TextFace("ABCDEFGHIJK"[0:random.randint(1,11)])
            F.border.width = 1
            F.border.line_style = 1
            F.inner_background.color = "lightgreen"
            F.border.width = 1
            F.inner_border.width = 1
            F.background.color = "darkgreen"
            F.border.width = 2
            F.vt_align = random.randint(0,4)
            F.hz_align = random.randint(0,4)
            F.margin_bottom = random.randint(1, 20)
            F.margin_right  = random.randint(1, 20)
            F.margin_left = random.randint(1, 20)
            F.margin_top = random.randint(1, 20)

            faces.add_face_to_node(F, node, i, position="aligned")
            if random.randint(0, 1):
                faces.add_face_to_node(F, node, i, position="aligned")
コード例 #41
0
def layout(node):
    if node.is_leaf():
        F = faces.PieChartFace(
            [10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 6], colors=COLOR_SCHEMES["set3"], width=50, height=50
        )
        F.border.width = None
        F.opacity = 0.8
        faces.add_face_to_node(F, node, 0, position="branch-right")

        F = faces.PieChartFace(
            [10, 20, 5, 5, 60], colors=COLOR_SCHEMES[random.sample(schema_names, 1)[0]], width=100, height=40
        )
        F.border.width = None
        F.opacity = 0.8
        faces.add_face_to_node(F, node, 0, position="branch-right")
    else:
        F = faces.BarChartFace(
            [40, 20, 70, 100, 30, 40, 50, 40, 70, -12],
            min_value=-12,
            colors=COLOR_SCHEMES["spectral"],
            labels="aaa,bbb,cccccc,dd,eeee,ffff,gg,HHH,II,JJJ,KK".split(","),
            label_fsize=10,
            scale_fsize=10,
        )
        faces.add_face_to_node(F, node, 0, position="branch-top")
        F.background.color = "#eee"
コード例 #42
0
def phyparts_pie_layout(mynode):
    if mynode.name in phyparts_pies:
        pie= faces.PieChartFace(phyparts_pies[mynode.name],
                              #colors=COLOR_SCHEMES["set1"],
                              colors = args.colors,
                              width=50, height=50)
        pie.border.width = None
        pie.opacity = 1
        faces.add_face_to_node(pie,mynode, 0, position="branch-right")
        
        concord_text = faces.TextFace(str(int(concord_dict[mynode.name]))+'   ',fsize=20)
        conflict_text = faces.TextFace(str(int(conflict_dict[mynode.name]))+'   ',fsize=20)
        
        faces.add_face_to_node(concord_text,mynode,0,position = "branch-top")
        faces.add_face_to_node(conflict_text,mynode,0,position="branch-bottom")
        
        
    else:
        F = faces.TextFace(mynode.name,fsize=20)
        faces.add_face_to_node(F,mynode,0,position="aligned")
コード例 #43
0
 def layout(node):
     node.img_style['size'] = 0
     node.img_style['vt_line_width'] = 0
     node.img_style['hz_line_width'] = 0
     if "bgcolor" in node.features:
         node.img_style['bgcolor'] = node.bgcolor
     if node.is_leaf():
         if not args.no_names:
             name = faces.TextFace(node.sci_name, fsize=12, fstyle='italic')
             faces.add_face_to_node(name, node, 0, aligned=True)
         fake = faces.TextFace(" ")
         fake.background.color = "white"
         faces.add_face_to_node(fake, node, 1, aligned=True) # fake
     else:
         if not args.no_internal_names and node.get_distance(tNCBI, topology_only=True) < 3:
             name = faces.TextFace(node.sci_name, fsize=12, fstyle='italic')
             faces.add_face_to_node(name, node, 0, position='branch-top')
コード例 #44
0
ファイル: visualize_core.py プロジェクト: richrr/coremicro
 def layout(node):
     '''
     The layout function for exporting treees
     '''
     # Label the leaves
     if node.is_leaf():
         faces.add_face_to_node(TextFace(
             getattr(node, TAXA_FEATURE)[-1],
             fgcolor=('blue'
                      if getattr(node, GROUP_FEATURE) == interest_group
                      else 'black')),
                                node, column=0)
         pval = float(getattr(node, CORRECTED_P_VAL_FEATURE))
         pval_color = get_color(pval)
         faces.add_face_to_node(RectFace(10, 10, fgcolor='Black',
                                         bgcolor=pval_color),
                                node, column=1, aligned=True)
         faces.add_face_to_node(
             TextFace('  {0:0.5f}  {1}'.format(
                 float(getattr(node, CORRECTED_P_VAL_FEATURE)),
                 getattr(node, OTU_FEATURE))),
             node, column=2, aligned=True)
コード例 #45
0
ファイル: node_style.py プロジェクト: AlishaMechtley/ete
def layout(node):
    # If node is a leaf, add the nodes name and a its scientific name
    if node.is_leaf():
        faces.add_face_to_node(AttrFace("name"), node, column=0)
コード例 #46
0
ファイル: node_background.py プロジェクト: AlishaMechtley/ete
def layout(node):
    if node.is_leaf():
        N = AttrFace("name", fsize=30)
        faces.add_face_to_node(N, node, 0, position="aligned")
コード例 #47
0
def node_text_layout(mynode):
	F = faces.TextFace(mynode.name,fsize=20)
	faces.add_face_to_node(F,mynode,0,position="branch-right")
コード例 #48
0
ファイル: random_draw.py プロジェクト: AlishaMechtley/ete
def sphere_map(node):
    # Creates a random color sphere face that will be floating over nodes
    bubble = faces.CircleFace(random.randint(5,40), random_color(), "sphere")
    bubble.opacity = 0.7
    faces.add_face_to_node(bubble, node, 0, position="float")
コード例 #49
0
ファイル: random_draw.py プロジェクト: AlishaMechtley/ete
def leaf_name(node):
    if node.is_leaf():
        nameF = faces.AttrFace("name")
        nameF.border.width = 1
        faces.add_face_to_node(nameF, node, 0, position="branch-right")
コード例 #50
0
ファイル: node.py プロジェクト: mlberkeley/genetic-algs
 def layout(node):
     faces.add_face_to_node(AttrFace("name"), node, column=0,
                            position="branch-right")
コード例 #51
0
ファイル: random_draw.py プロジェクト: AlishaMechtley/ete
def test(node):
    if node.is_leaf():
        faces.add_face_to_node(faces.AttrFace("name"), node, 0, position="aligned")
コード例 #52
0
    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
コード例 #53
0
ファイル: img_faces.py プロジェクト: AlishaMechtley/ete
def mylayout(node):
    # If node is a leaf, add the nodes name and a its scientific
    # name
    if node.is_leaf():
        # Add an static face that handles the node name
        faces.add_face_to_node(nameFace, node, column=0)
        # We can also create faces on the fly
        longNameFace = faces.TextFace(code2name[node.name])
        faces.add_face_to_node(longNameFace, node, column=0)

        # text faces support multiline. We add a text face
        # with the whole description of each leaf.
        descFace = faces.TextFace(code2desc[node.name], fsize=10)
        descFace.margin_top = 10
        descFace.margin_bottom = 10
        descFace.border.margin = 1

        # Note that this faces is added in "aligned" mode
        faces.add_face_to_node(descFace, node, column=0, aligned=True)

        # Sets the style of leaf nodes
        node.img_style["size"] = 12
        node.img_style["shape"] = "circle"
    #If node is an internal node
    else:
        # Sets the style of internal nodes
        node.img_style["size"] = 6
        node.img_style["shape"] = "circle"
        node.img_style["fgcolor"] = "#000000"

    # If an internal node contains more than 4 leaves, add the
    # images of the represented species sorted in columns of 2
    # images max.
    if len(node)>=4:
        col = 0
        for i, name in enumerate(set(node.get_leaf_names())):
            if i>0 and i%2 == 0:
                col += 1
            # Add the corresponding face to the node
            if name.startswith("Dme"):
                faces.add_face_to_node(flyFace, node, column=col)
            elif name.startswith("Dre"):
                faces.add_face_to_node(fishFace, node, column=col)
            elif name.startswith("Mms"):
                faces.add_face_to_node(mouseFace, node, column=col)
            elif name.startswith("Ptr"):
                faces.add_face_to_node(chimpFace, node, column=col)
            elif name.startswith("Hsa"):
                faces.add_face_to_node(humanFace, node, column=col)
            elif name.startswith("Cfa"):
                faces.add_face_to_node(dogFace, node, column=col)

            # Modifies this node's style
            node.img_style["size"] = 16
            node.img_style["shape"] = "sphere"
            node.img_style["fgcolor"] = "#AA0000"

    # If leaf is "Hsa" (h**o sapiens), highlight it using a
    # different background.
    if node.is_leaf() and node.name.startswith("Hsa"):
        node.img_style["bgcolor"] = "#9db0cf"
コード例 #54
0
ファイル: webplugin_example.py プロジェクト: abdo3a/ete
def main_layout(node):
    ''' Main layout function. It controls what is shown in tree
    images. '''

    # Add faces to leaf nodes. This allows me to add the faces from
    # the global variable LEAVE_FACES, which is set by the application
    # controler according to the arguments passed through the URL.
    if node.is_leaf():

        for f, fkey, pos in LEAVE_FACES:
            if hasattr(node, fkey):
                faces.add_face_to_node(f, node, column=pos, position="branch-right")
    else:
        # Add special faces on collapsed nodes
        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


    # Set node aspect. This controls which node features are used to
    # control the style of the tree. You can add or modify this
    # features, as well as their behaviour
    if node.is_leaf():
        node.img_style["shape"] = "square"
        node.img_style["size"] = 4
    else:
        node.img_style["size"] = 8
        node.img_style["shape"] = "sphere"

    # Evoltype: [D]uplications, [S]peciations or [L]osess.
    if hasattr(node,"evoltype"):
        if node.evoltype == 'D':
            node.img_style["fgcolor"] = "#1d176e"
            node.img_style["hz_line_color"] = "#1d176e"
            node.img_style["vt_line_color"] = "#1d176e"
        elif node.evoltype == 'S':
            node.img_style["fgcolor"] = "#FF0000"
            node.img_style["line_color"] = "#FF0000"
        elif node.evoltype == 'L':
            node.img_style["fgcolor"] = "#777777"
            node.img_style["vt_line_color"] = "#777777"
            node.img_style["hz_line_color"] = "#777777"
            node.img_style["line_type"] = 1
    # If no evolutionary information, set a default style
    else:
        node.img_style["fgcolor"] = "#000000"
        node.img_style["vt_line_color"] = "#000000"
        node.img_style["hz_line_color"] = "#000000"

    # 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