Exemple #1
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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")
Exemple #2
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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")
Exemple #3
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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")
Exemple #4
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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")
Exemple #5
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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")
Exemple #6
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def layout(node):
    global CONT
    if CONT >= len(chars):
        CONT = 0
    if node.is_leaf():
        node.img_style["size"] = 0
        F2= AttrFace("name", tight_text=True)
        F= TextFace(chars[CONT], tight_text=True)
        F.inner_border.width = 0
        F2.inner_border.width = 0
        #faces.add_face_to_node(F ,node, 0, position="branch-right")
        faces.add_face_to_node(F2 ,node, 1, position="branch-right")
        CONT += 1
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)
Exemple #8
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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")
Exemple #9
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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)

        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")
Exemple #10
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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)
Exemple #11
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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)
Exemple #12
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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)

        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")
Exemple #13
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def layout(node):
    node.img_style["size"] = random.randint(5, 100)
    node.img_style["hz_line_width"] = 5
    node.img_style["vt_line_width"] = 10
    if node.is_leaf():
        # node.img_style["size"] = random.randint(50, 50)
        f = faces.TextFace("alignedFace", fsize=8, fgcolor="blue")
        # f = faces.AttrFace("name", fsize=random.randint(20,20))
        faces.add_face_to_node(f, node, 0, position="aligned")
        f.border.width = 0
        # f = faces.CircleFace(20, "red")
        # f = faces.AttrFace("name", fsize=20)
        f = faces.TextFace("NAME", fsize=10)
        # faces.add_face_to_node(f, node, 0, position="branch-right")
        f.border.width = 0
Exemple #14
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def layout2(node):
    #node.img_style["size"] = random.randint(40, 200)
    if hasattr(node, "size"):
        f = faces.PieChartFace([100], node.size[0], node.size[1], ["blue"])
        faces.add_face_to_node(f, node, 0, position="branch-top")
        faces.add_face_to_node(f, node, 0, position="branch-bottom")
        #f = faces.PieChartFace([100], node.size[0]*3, node.size[0]*3, ["blue"])
        #faces.add_face_to_node(f, node, 0, position="branch-right")
        f.border.width = 0

        node.img_style["size"] = 10
        node.img_style["shape"] = "square"
    node.img_style["bgcolor"] = random_color()
    node.img_style["hz_line_width"] = 0
    node.img_style["vt_line_width"] = 0
Exemple #15
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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)
Exemple #16
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def layout(node):
    node.img_style["size"] = random.randint(5,100)
    node.img_style["hz_line_width"] = 5
    node.img_style["vt_line_width"] = 10
    if node.is_leaf():
        #node.img_style["size"] = random.randint(50, 50)
        f = faces.TextFace("alignedFace", fsize=8, fgcolor="blue")
        #f = faces.AttrFace("name", fsize=random.randint(20,20))
        faces.add_face_to_node(f, node, 0, position="aligned")
        f.border.width = 0
        #f = faces.CircleFace(20, "red")
        #f = faces.AttrFace("name", fsize=20)
        f = faces.TextFace("NAME", fsize=10)
        #faces.add_face_to_node(f, node, 0, position="branch-right")
        f.border.width = 0
Exemple #17
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def layout2(node):
    #node.img_style["size"] = random.randint(40, 200)
    if hasattr(node, "size"):
        f = faces.PieChartFace([100], node.size[0], node.size[1], ["blue"])
        faces.add_face_to_node(f, node, 0, position="branch-top")
        faces.add_face_to_node(f, node, 0, position="branch-bottom")
        #f = faces.PieChartFace([100], node.size[0]*3, node.size[0]*3, ["blue"])
        #faces.add_face_to_node(f, node, 0, position="branch-right")
        f.border.width = 0
        
        node.img_style["size"] = 10
        node.img_style["shape"] = "square"
    node.img_style["bgcolor"] = random_color()
    node.img_style["hz_line_width"] = 0
    node.img_style["vt_line_width"] = 0
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)
Exemple #19
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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)
Exemple #20
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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")
Exemple #21
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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")
Exemple #22
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def ncbi_layout(node):
    npr_layout(node)
    global name2color
    if node.is_leaf():
        tax_pos = 10
        if hasattr(node, "lineage"):
            for tax, k in zip(node.lineage, node.named_lineage):
                f = faces.TextFace("%10s" % k, fsize=15)
                try:
                    color = name2color[k]
                except KeyError:
                    name2color[k] = color = treeview.main.random_color()

                #if hasattr(node, "broken_groups") and tax in node.broken_groups:
                f.background.color = color
                faces.add_face_to_node(f, node, tax_pos, position="aligned")
                tax_pos += 1

            f = faces.AttrFace("spname", fsize=15)
            faces.add_face_to_node(f, node, 10, position="branch-right")
    else:
        if getattr(node, "broken_groups", None):
            for broken in node.broken_groups:
                f = faces.TextFace(broken, fsize=10, fgcolor="red")
                faces.add_face_to_node(f, node, 1, position="branch-bottom")

    if hasattr(node, "changed"):
        if node.changed == "yes":
            node.img_style["bgcolor"] = "indianred"
        else:
            node.img_style["bgcolor"] = "white"
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=0,
            colors=COLOR_SCHEMES["spectral"],
            labels="aaa,bbb,cccccc,dd,eeee,ffff,gg,HHH,II,JJJ,KK".split(","))
        faces.add_face_to_node(F, node, 0, position="branch-top")
        F.background.color = "#eee"
def ncbi_layout(node):
    npr_layout(node)
    global name2color
    if node.is_leaf():
        tax_pos = 10
        if hasattr(node, "lineage"):
            for tax,k in zip(node.lineage, node.named_lineage):
                f = faces.TextFace("%10s" %k, fsize=15)
                try:
                    color = name2color[k]
                except KeyError:
                    name2color[k] = color = treeview.main.random_color()

                #if hasattr(node, "broken_groups") and tax in node.broken_groups:
                f.background.color = color
                faces.add_face_to_node(f, node, tax_pos, position="aligned")
                tax_pos += 1
                    
            f = faces.AttrFace("spname", fsize=15)
            faces.add_face_to_node(f, node, 10, position="branch-right")
    else:
        if getattr(node, "broken_groups", None):
            for broken in node.broken_groups:
                f = faces.TextFace(broken, fsize=10, fgcolor="red")
                faces.add_face_to_node(f, node, 1, position="branch-bottom")

    if hasattr(node, "changed"):
        if node.changed == "yes":
            node.img_style["bgcolor"]="indianred"
        else:
            node.img_style["bgcolor"]="white"
Exemple #25
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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=100, height=100)
        F.border.width = None
        F.opacity = 0.8
        faces.add_face_to_node(F,node, 0, position="branch-right")
        F.background.color = "indianred"
        x = faces.TextFace("hola")
        faces.add_face_to_node(x,node, 1, position="branch-right")
        x.background.color = "blue"
    else:
        F= faces.BarChartFace([40,20,70,100,30,40,50,40,70,12], min_value=0, colors=COLOR_SCHEMES["spectral"])
        faces.add_face_to_node(F,node, 0, position="branch-top")
Exemple #26
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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=100,
                               height=100)
        F.border.width = None
        F.opacity = 0.8
        faces.add_face_to_node(F, node, 0, position="branch-right")
        F.background.color = "indianred"
        x = faces.TextFace("hola")
        faces.add_face_to_node(x, node, 1, position="branch-right")
        x.background.color = "blue"
    else:
        F = faces.BarChartFace([40, 20, 70, 100, 30, 40, 50, 40, 70, 12],
                               min_value=0,
                               colors=COLOR_SCHEMES["spectral"])
        faces.add_face_to_node(F, node, 0, position="branch-top")
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=0,
            colors=COLOR_SCHEMES["spectral"],
            labels="aaa,bbb,cccccc,dd,eeee,ffff,gg,HHH,II,JJJ,KK".split(","),
        )
        faces.add_face_to_node(F, node, 0, position="branch-top")
        F.background.color = "#eee"
Exemple #28
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def layout(node):
    node.img_style["size"] = 5
    node.img_style["hz_line_width"] = 0
    node.img_style["vt_line_width"] = 0
    if node.is_leaf():
        f = faces.AttrFace("name", fgcolor="steelblue", fsize=20)
        faces.add_face_to_node(f, node, 0, position="aligned")

        f = faces.AttrFace("name", fsize=15)
        faces.add_face_to_node(f, node, 0, position="branch-right")
    else:
        f = faces.TextFace("uno", fsize=8)
        for x in xrange(random.randint(1, 5)):
            faces.add_face_to_node(f, node, 0, position="branch-top")

        f = faces.TextFace("otromassssssssssss", fsize=8)
        for x in xrange(random.randint(1, 5)):
            faces.add_face_to_node(f, node, 0, position="branch-bottom")

    f = faces.CircleFace(20, "red")
    f.opacity = 0.3
    faces.add_face_to_node(f, node, 0, position="float")
    f = faces.CircleFace(23, "blue")
    f.opacity = 0.3
    faces.add_face_to_node(f, node, 0, position="float-behind")
Exemple #29
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def test(node):
    if node.is_leaf():
        faces.add_face_to_node(faces.AttrFace("name"), node, 0, position="aligned")
Exemple #30
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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)
        # 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"
Exemple #31
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def npr_layout(node):
    if node.is_leaf():
        name = faces.AttrFace("name", fsize=12)
        faces.add_face_to_node(name, node, 0, position="branch-right")
        if hasattr(node, "sequence"):
            seq_face = faces.SeqFace(node.sequence, [])
            faces.add_face_to_node(seq_face, node, 0, position="aligned")

    if "alg_type" in node.features:
        faces.add_face_to_node(faces.AttrFace("alg_type", fsize=8),
                               node,
                               0,
                               position="branch-top")
        ttype = faces.AttrFace("tree_type", fsize=8, fgcolor="DarkBlue")
        faces.add_face_to_node(ttype, node, 0, position="branch-top")
        #ttype.background.color = "DarkOliveGreen"
        node.img_style["size"] = 20
        node.img_style["fgcolor"] = "red"

    if "treemerger_rf" in node.features:
        faces.add_face_to_node(faces.AttrFace("treemerger_rf", fsize=8),
                               node,
                               0,
                               position="branch-bottom")

    support_radius = (1.0 - node.support) * 50
    if not node.is_leaf() and support_radius > 1:
        support_face = faces.CircleFace(support_radius, "red")
        faces.add_face_to_node(support_face, node, 0, position="float-behind")
        support_face.opacity = 0.25
        faces.add_face_to_node(faces.AttrFace("support", fsize=8),
                               node,
                               0,
                               position="branch-bottom")

    if "clean_alg_mean_identn" in node.features:
        identity = node.clean_alg_mean_identn
    elif "alg_mean_identn" in node.features:
        identity = node.alg_mean_identn

    if "highlighted" in node.features:
        node.img_style["bgcolor"] = "LightCyan"

    if "improve" in node.features:
        color = "orange" if float(node.improve) < 0 else "green"
        if float(node.improve) == 0:
            color = "blue"

        support_face = faces.CircleFace(200, color)
        faces.add_face_to_node(support_face, node, 0, position="float-behind")
Exemple #32
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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")
Exemple #33
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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")
Exemple #34
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def mylayout(node):
    T = TestTreeview
    node.img_style["size"]=random.sample(range(4,30),1)[0]
    if node.is_leaf():
        faces.add_face_to_node(T.nameF, node, column=0, position="aligned")
        faces.add_face_to_node(T.nameF, node, column=2, position="aligned")
        faces.add_face_to_node(T.nameF, node, column=3, position="aligned")
    else:
        faces.add_face_to_node(T.topF, node, column=1, position="branch-top")
        faces.add_face_to_node(T.topF, node, column=1, position="branch-top")
        faces.add_face_to_node(T.topF, node, column=1, position="branch-top")
        faces.add_face_to_node(T.topF, node, column=1, position="branch-top")
        faces.add_face_to_node(T.downF, node, column=1, position="branch-bottom")
        faces.add_face_to_node(T.downF, node, column=1, position="branch-bottom")
        faces.add_face_to_node(T.rF1, node, column=1, position="branch-right")
        faces.add_face_to_node(T.rF2, node, column=1, position="branch-right")
        faces.add_face_to_node(T.rF3, node, column=2, position="branch-right")
def npr_layout(node):
    if node.is_leaf():
        name = faces.AttrFace("name", fsize=12)
        faces.add_face_to_node(name, node, 0, position="branch-right")
        if hasattr(node, "sequence"):
            seq_face = faces.SeqFace(node.sequence, [])
            faces.add_face_to_node(seq_face, node, 0, position="aligned")

        
    if "alg_type" in node.features:
        faces.add_face_to_node(faces.AttrFace("alg_type", fsize=8), node, 0, position="branch-top")
        ttype=faces.AttrFace("tree_type", fsize=8, fgcolor="DarkBlue")
        faces.add_face_to_node(ttype, node, 0, position="branch-top")
        #ttype.background.color = "DarkOliveGreen"
        node.img_style["size"] = 20
        node.img_style["fgcolor"] = "red"
        
    if "treemerger_rf" in node.features:
        faces.add_face_to_node(faces.AttrFace("treemerger_rf", fsize=8), node, 0, position="branch-bottom")

    support_radius= (1.0 - node.support) * 50
    if not node.is_leaf() and support_radius > 1:
        support_face = faces.CircleFace(support_radius, "red")
        faces.add_face_to_node(support_face, node, 0, position="float-behind")
        support_face.opacity = 0.25
        faces.add_face_to_node(faces.AttrFace("support", fsize=8), node, 0, position="branch-bottom")
        

    if "clean_alg_mean_identn" in node.features:
        identity = node.clean_alg_mean_identn
    elif "alg_mean_identn" in node.features:
        identity = node.alg_mean_identn

    if "highlighted" in node.features:
        node.img_style["bgcolor"] = "LightCyan"

    if "improve" in node.features:
        color = "orange" if float(node.improve) < 0 else "green"
        if float(node.improve) == 0:
            color = "blue"
             
        support_face = faces.CircleFace(200, color)        
        faces.add_face_to_node(support_face, node, 0, position="float-behind")
Exemple #36
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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)
Exemple #37
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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
Exemple #38
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def mylayout(node):
    # If node is a leaf, add the nodes name and a its scientific
    # name
    if node.is_leaf():
        faces.add_face_to_node(aligned, node, column=0, position="aligned")
        faces.add_face_to_node(aligned, node, column=1, position="aligned")
        faces.add_face_to_node(aligned, node, column=3, position="aligned")
    else:
        faces.add_face_to_node(bt, node, column=0, position="branch-top")
        faces.add_face_to_node(bb, node, column=0, position="branch-bottom")
        faces.add_face_to_node(bb2, node, column=0, position="branch-bottom")
        faces.add_face_to_node(br1, node, column=0, position="branch-right")
        faces.add_face_to_node(rs1, node, column=0, position="branch-right")
        faces.add_face_to_node(br2, node, column=0, position="branch-right")
Exemple #39
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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)
Exemple #40
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def layout(node):
    node.img_style["size"] = 5
    node.img_style["hz_line_width"] = 0
    node.img_style["vt_line_width"] = 0
    if node.is_leaf():
        f = faces.AttrFace("name", fgcolor="steelblue", fsize=20)
        faces.add_face_to_node(f, node, 0, position="aligned")
        
        f = faces.AttrFace("name", fsize=15)
        faces.add_face_to_node(f, node, 0, position="branch-right")
    else:
        f = faces.TextFace("uno", fsize=8)
        for x in xrange(random.randint(1, 5)):
            faces.add_face_to_node(f, node, 0, position="branch-top")

        f = faces.TextFace("otromassssssssssss", fsize=8)
        for x in xrange(random.randint(1, 5)):
            faces.add_face_to_node(f, node, 0, position="branch-bottom")
        
    f = faces.CircleFace(20, "red")
    f.opacity = 0.3
    faces.add_face_to_node(f, node, 0, position="float")
    f = faces.CircleFace(23, "blue")
    f.opacity = 0.3
    faces.add_face_to_node(f, node, 0, position="float-behind")
Exemple #41
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def layout(node):
    if node.is_leaf():
        N = AttrFace("name", fsize=30)
        faces.add_face_to_node(N, node, 0, position="aligned")
Exemple #42
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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")
Exemple #43
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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
Exemple #44
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def codeml_clean_layout(node):
    '''
    layout for CodemlTree
    '''
    for f, fkey, pos in LEAVE_FACES:
        if hasattr(node, fkey):
            if not (fkey == 'name' and node.name == 'NoName'):
                if node.is_leaf():
                    faces.add_face_to_node(f,
                                           node,
                                           column=pos,
                                           position="branch-right")
                elif fkey == 'species':
                    if node.species != "Unknown":
                        faces.add_face_to_node(faces.TextFace(
                            ' (%s)' % (node.species),
                            fsize=6,
                            fgcolor="#787878"),
                                               node,
                                               -1,
                                               position="branch-bottom")
                else:
                    faces.add_face_to_node(f,
                                           node,
                                           column=pos,
                                           position="branch-bottom")
    if hasattr(node, 'dN'):
        faces.add_face_to_node(faces.TextFace('%.4f' % (node.w),
                                              fsize=6,
                                              fgcolor="#7D2D2D"),
                               node,
                               0,
                               position="branch-top")
        faces.add_face_to_node(faces.TextFace('%.2f/%.2f' %
                                              (100 * node.dN, 100 * node.dS),
                                              fsize=6,
                                              fgcolor="#787878"),
                               node,
                               0,
                               position="branch-bottom")
    if not node.is_leaf():
        node.img_style["shape"] = "sphere"
        node.img_style["size"] = 5
        # 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
    else:
        node.img_style["size"] = 2
        node.img_style["shape"] = "square"
        if hasattr(node, "sequence"):
            seqface = faces.SequenceFace(node.sequence, "aa", 11)
            faces.add_face_to_node(seqface, node, 1, aligned=True)
    leaf_color = "#000000"
    node.img_style["fgcolor"] = leaf_color
    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
Exemple #45
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def layout(node):
    if node.is_leaf():
        N = AttrFace("name", fsize=30)
        faces.add_face_to_node(N, node, 0, position="aligned")
Exemple #46
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def test(node):
    if node.is_leaf():
        faces.add_face_to_node(faces.AttrFace("name"),
                               node,
                               0,
                               position="aligned")
Exemple #47
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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"
Exemple #48
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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")