Plot API Example

In [1]:

# %pip install phytreeviz

# %pip install phytreeviz

show_branch_length¶

In [2]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file)
tv.show_branch_length(label_formatter=lambda v: f"{v:.4f}")

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file) tv.show_branch_length(label_formatter=lambda v: f"{v:.4f}") fig = tv.plotfig()

show_confidence¶

In [3]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file)
tv.show_confidence(ypos="top", label_formatter=lambda v: f"{v:.2f}")

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file) tv.show_confidence(ypos="top", label_formatter=lambda v: f"{v:.2f}") fig = tv.plotfig()

show_scale_axis¶

In [4]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file, align_leaf_label=True)
tv.show_scale_axis(ticks_interval=0.1)

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file, align_leaf_label=True) tv.show_scale_axis(ticks_interval=0.1) fig = tv.plotfig()

show_scale_bar¶

In [5]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file)
tv.show_scale_bar()
tv.show_scale_bar(scale_size=0.1, loc="upper left", label_top=True)

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file) tv.show_scale_bar() tv.show_scale_bar(scale_size=0.1, loc="upper left", label_top=True) fig = tv.plotfig()

highlight¶

In [6]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file, align_leaf_label=True)

tv.highlight(["Hylobates_moloch", "Nomascus_leucogenys"], "orange", area="branch")
tv.highlight("Pongo_abelii", "pink", area="branch-label")
tv.highlight(["Homo_sapiens", "Pan_paniscus"], "lime", area="full")

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file, align_leaf_label=True) tv.highlight(["Hylobates_moloch", "Nomascus_leucogenys"], "orange", area="branch") tv.highlight("Pongo_abelii", "pink", area="branch-label") tv.highlight(["Homo_sapiens", "Pan_paniscus"], "lime", area="full") fig = tv.plotfig()

annotate¶

In [7]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file)

tv.annotate(["Hylobates_moloch", "Nomascus_leucogenys"], "group1", line_color="orange")
tv.annotate("Pongo_abelii", "group2", align=True, line_color="red")
tv.annotate("Gorilla_gorilla_gorilla", "group3", align=True, line_color="blue")
tv.annotate(["Homo_sapiens", "Pan_paniscus"], "group4", line_color="lime", text_orientation="vertical")

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file) tv.annotate(["Hylobates_moloch", "Nomascus_leucogenys"], "group1", line_color="orange") tv.annotate("Pongo_abelii", "group2", align=True, line_color="red") tv.annotate("Gorilla_gorilla_gorilla", "group3", align=True, line_color="blue") tv.annotate(["Homo_sapiens", "Pan_paniscus"], "group4", line_color="lime", text_orientation="vertical") fig = tv.plotfig()

marker¶

In [8]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file, align_leaf_label=True, leaf_label_xmargin_ratio=0.02)

tv.marker(["Hylobates_moloch", "Nomascus_leucogenys"], color="blue")
tv.marker("Pongo_abelii", marker="s", color="red")
tv.marker(["Homo_sapiens", "Pan_paniscus"], marker="D", descendent=True, fc="lime", ec="black", lw=0.5)

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file, align_leaf_label=True, leaf_label_xmargin_ratio=0.02) tv.marker(["Hylobates_moloch", "Nomascus_leucogenys"], color="blue") tv.marker("Pongo_abelii", marker="s", color="red") tv.marker(["Homo_sapiens", "Pan_paniscus"], marker="D", descendent=True, fc="lime", ec="black", lw=0.5) fig = tv.plotfig()

link¶

In [9]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file, align_leaf_label=True)

tv.link("Pongo_abelii", ["Hylobates_moloch", "Nomascus_leucogenys"])
tv.link(
    "Homo_sapiens",
    ["Pan_troglodytes", "Pan_paniscus"],
    color="blue",
    arrowstyle="<|-|>",
    connectionstyle="arc3,rad=0.2",
)

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file, align_leaf_label=True) tv.link("Pongo_abelii", ["Hylobates_moloch", "Nomascus_leucogenys"]) tv.link( "Homo_sapiens", ["Pan_troglodytes", "Pan_paniscus"], color="blue", arrowstyle="<|-|>", connectionstyle="arc3,rad=0.2", ) fig = tv.plotfig()

text_on_branch¶

In [10]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file, align_leaf_label=True)

tv.text_on_branch(["Hylobates_moloch", "Nomascus_leucogenys"], text="Node01")
tv.text_on_branch("Pongo_abelii", text="Node02", xpos="left", ypos="bottom", color="red")
tv.text_on_branch(
    ["Pan_troglodytes", "Pan_paniscus"],
    text="Node03",
    xpos="center",
    ypos="center",
    bbox=dict(boxstyle="square,pad=0.3", fc="skyblue")
)

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file, align_leaf_label=True) tv.text_on_branch(["Hylobates_moloch", "Nomascus_leucogenys"], text="Node01") tv.text_on_branch("Pongo_abelii", text="Node02", xpos="left", ypos="bottom", color="red") tv.text_on_branch( ["Pan_troglodytes", "Pan_paniscus"], text="Node03", xpos="center", ypos="center", bbox=dict(boxstyle="square,pad=0.3", fc="skyblue") ) fig = tv.plotfig()

text_on_node¶

In [11]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file, align_leaf_label=True)

tv.marker(["Hylobates_moloch", "Nomascus_leucogenys"], fc="lime", ec="black", lw=0.5, size=10)
tv.text_on_node(["Hylobates_moloch", "Nomascus_leucogenys"], "1")
tv.text_on_node(
    ["Pan_troglodytes", "Pan_paniscus"],
    text="Node",
    bbox=dict(boxstyle="square,pad=0.3", fc="skyblue")
)

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file, align_leaf_label=True) tv.marker(["Hylobates_moloch", "Nomascus_leucogenys"], fc="lime", ec="black", lw=0.5, size=10) tv.text_on_node(["Hylobates_moloch", "Nomascus_leucogenys"], "1") tv.text_on_node( ["Pan_troglodytes", "Pan_paniscus"], text="Node", bbox=dict(boxstyle="square,pad=0.3", fc="skyblue") ) fig = tv.plotfig()

set_node_label_props¶

In [12]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file, align_leaf_label=True)

tv.set_node_label_props("Hylobates_moloch", color="blue")
tv.set_node_label_props("Pongo_abelii", color="red", style="italic")
tv.set_node_label_props("Homo_sapiens", size=8, backgroundcolor="lime")

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file, align_leaf_label=True) tv.set_node_label_props("Hylobates_moloch", color="blue") tv.set_node_label_props("Pongo_abelii", color="red", style="italic") tv.set_node_label_props("Homo_sapiens", size=8, backgroundcolor="lime") fig = tv.plotfig()

set_node_line_props¶

In [13]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")
tv = TreeViz(tree_file)

tv.set_node_line_props(["Hylobates_moloch", "Nomascus_leucogenys"], color="orange", lw=2)
tv.set_node_line_props(["Homo_sapiens", "Pan_paniscus"], color="magenta", ls="dotted")

fig = tv.plotfig()

from phytreeviz import TreeViz, load_example_tree_file tree_file = load_example_tree_file("small_example.nwk") tv = TreeViz(tree_file) tv.set_node_line_props(["Hylobates_moloch", "Nomascus_leucogenys"], color="orange", lw=2) tv.set_node_line_props(["Homo_sapiens", "Pan_paniscus"], color="magenta", ls="dotted") fig = tv.plotfig()