Getting Started

In [1]:

# %pip install phytreeviz

# %pip install phytreeviz

Example1¶

Show branch length, confidence value, scale bar

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(color="red")
tv.show_confidence(color="blue")
tv.show_scale_bar()

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(color="red") tv.show_confidence(color="blue") tv.show_scale_bar() fig = tv.plotfig()

Example2¶

• Set plot properties of label text and branch line
• Show scale axis

In [3]:

from phytreeviz import TreeViz, load_example_tree_file

tree_file = load_example_tree_file("small_example.nwk")

tv = TreeViz(tree_file, height=0.7)
tv.show_scale_axis()

tv.set_node_label_props("Homo_sapiens", color="grey")
tv.set_node_label_props("Pongo_abelii", color="green", style="italic")

tv.set_node_line_props(["Hylobates_moloch", "Nomascus_leucogenys"], color="orange", lw=2)
tv.set_node_line_props(["Homo_sapiens", "Pan_troglodytes", "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, height=0.7) tv.show_scale_axis() tv.set_node_label_props("Homo_sapiens", color="grey") tv.set_node_label_props("Pongo_abelii", color="green", style="italic") tv.set_node_line_props(["Hylobates_moloch", "Nomascus_leucogenys"], color="orange", lw=2) tv.set_node_line_props(["Homo_sapiens", "Pan_troglodytes", "Pan_paniscus"], color="magenta", ls="dotted") fig = tv.plotfig()

Example3¶

• Align leaf label position to rightmost
• Plot highlight and annotation for groups
• Plot marker for target taxa

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()

group1 = ["Hylobates_moloch", "Nomascus_leucogenys"]
group2 = ["Homo_sapiens", "Pan_paniscus"]

tv.highlight(group1, "orange")
tv.highlight(group2, "lime")

tv.annotate(group1, "group1")
tv.annotate(group2, "group2")

tv.marker(group1, marker="s", color="blue")
tv.marker(group2, marker="D", color="purple", descendent=True)
tv.marker("Pongo_abelii", color="red")

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() group1 = ["Hylobates_moloch", "Nomascus_leucogenys"] group2 = ["Homo_sapiens", "Pan_paniscus"] tv.highlight(group1, "orange") tv.highlight(group2, "lime") tv.annotate(group1, "group1") tv.annotate(group2, "group2") tv.marker(group1, marker="s", color="blue") tv.marker(group2, marker="D", color="purple", descendent=True) tv.marker("Pongo_abelii", color="red") fig = tv.plotfig()

Example4¶

• Plot highlight and legend for groups
• Plot link between target clades

In [5]:

from phytreeviz import TreeViz, load_example_tree_file
from matplotlib.patches import Patch

tree_file = load_example_tree_file("medium_example.nwk")

tv = TreeViz(tree_file, height=0.3, align_leaf_label=True, leaf_label_size=10)
tv.show_scale_bar()

group1 = ["Hylobates_moloch", "Nomascus_leucogenys"]
group2 = ["Homo_sapiens", "Pongo_abelii"]
group3 = ["Piliocolobus_tephrosceles", "Rhinopithecus_bieti"]
group4 = ["Chlorocebus_sabaeus", "Papio_anubis"]

tv.highlight(group1, "orange", area="full")
tv.highlight(group2, "skyblue", area="full")
tv.highlight(group3, "lime", area="full")
tv.highlight(group4, "pink", area="full")

tv.link(group3, group4, connectionstyle="arc3,rad=0.2")

fig = tv.plotfig()

_ = fig.legend(
    handles=[
        Patch(label="group1", color="orange"),
        Patch(label="group2", color="skyblue"),
        Patch(label="group3", color="lime"),
        Patch(label="group4", color="pink"),
    ],
    frameon=False,
    bbox_to_anchor=(0.3, 0.3),
    loc="center",
    ncols=2,
)

# fig.savefig("result.png", dpi=300)

from phytreeviz import TreeViz, load_example_tree_file from matplotlib.patches import Patch tree_file = load_example_tree_file("medium_example.nwk") tv = TreeViz(tree_file, height=0.3, align_leaf_label=True, leaf_label_size=10) tv.show_scale_bar() group1 = ["Hylobates_moloch", "Nomascus_leucogenys"] group2 = ["Homo_sapiens", "Pongo_abelii"] group3 = ["Piliocolobus_tephrosceles", "Rhinopithecus_bieti"] group4 = ["Chlorocebus_sabaeus", "Papio_anubis"] tv.highlight(group1, "orange", area="full") tv.highlight(group2, "skyblue", area="full") tv.highlight(group3, "lime", area="full") tv.highlight(group4, "pink", area="full") tv.link(group3, group4, connectionstyle="arc3,rad=0.2") fig = tv.plotfig() _ = fig.legend( handles=[ Patch(label="group1", color="orange"), Patch(label="group2", color="skyblue"), Patch(label="group3", color="lime"), Patch(label="group4", color="pink"), ], frameon=False, bbox_to_anchor=(0.3, 0.3), loc="center", ncols=2, ) # fig.savefig("result.png", dpi=300)