.. _imete3rst: ==== ete3 ==== .. only:: html **Links:** :download:`notebook `, :downloadlink:`html `, :download:`PDF `, :download:`python `, :downloadlink:`slides `, :githublink:`GitHub|_doc/notebooks/2016/pydata/im_ete3.ipynb|*` `ete3 `__ draws nice trees. `documentation `__ `source `__ `installation `__ `tutorial `__ `gallery `__ `notebook `__ .. code:: ipython3 from jyquickhelper import add_notebook_menu add_notebook_menu() .. contents:: :local: example ------- .. code:: ipython3 from ete3 import ClusterTree # Example of a minimalistic numerical matrix. It is encoded as a text # string for convenience, but it usally be loaded from a text file. matrix = """ #Names\tcol1\tcol2\tcol3\tcol4\tcol5\tcol6\tcol7 A\t-1.23\t-0.81\t1.79\t0.78\t-0.42\t-0.69\t0.58 B\t-1.76\t-0.94\t1.16\t0.36\t0.41\t-0.35\t1.12 C\t-2.19\t0.13\t0.65\t-0.51\t0.52\t1.04\t0.36 D\t-1.22\t-0.98\t0.79\t-0.76\t-0.29\t1.54\t0.93 E\t-1.47\t-0.83\t0.85\t0.07\t-0.81\t1.53\t0.65 F\t-1.04\t-1.11\t0.87\t-0.14\t-0.80\t1.74\t0.48 G\t-1.57\t-1.17\t1.29\t0.23\t-0.20\t1.17\t0.26 H\t-1.53\t-1.25\t0.59\t-0.30\t0.32\t1.41\t0.77 """ print("Example numerical matrix") print(matrix) .. parsed-literal:: Example numerical matrix #Names col1 col2 col3 col4 col5 col6 col7 A -1.23 -0.81 1.79 0.78 -0.42 -0.69 0.58 B -1.76 -0.94 1.16 0.36 0.41 -0.35 1.12 C -2.19 0.13 0.65 -0.51 0.52 1.04 0.36 D -1.22 -0.98 0.79 -0.76 -0.29 1.54 0.93 E -1.47 -0.83 0.85 0.07 -0.81 1.53 0.65 F -1.04 -1.11 0.87 -0.14 -0.80 1.74 0.48 G -1.57 -1.17 1.29 0.23 -0.20 1.17 0.26 H -1.53 -1.25 0.59 -0.30 0.32 1.41 0.77 .. code:: ipython3 t = ClusterTree("(((A,B),(C,(D,E))),(F,(G,H)));", text_array=matrix) print(t) .. parsed-literal:: /-A /-| | \-B /-| | | /-C | \-| | | /-D --| \-| | \-E | | /-F \-| | /-G \-| \-H .. code:: ipython3 t.render("%%inline", h=300) .. image:: im_ete3_6_0.png .. code:: ipython3 from ete3 import TreeStyle ts = TreeStyle() ts.show_branch_length = True # show branch length ts.show_branch_support = True # show support ts.show_leaf_name = True .. code:: ipython3 t.render("%%inline",tree_style=ts) .. image:: im_ete3_8_0.png .. code:: ipython3 ts.layout_fn = "heatmap" t.render("%%inline",tree_style=ts) .. image:: im_ete3_9_0.png .. code:: ipython3 ts.layout_fn = "cluster_cbars" t.render("%%inline",tree_style=ts) .. image:: im_ete3_10_0.png .. code:: ipython3 ts.layout_fn = "cluster_bars" t.render("%%inline",tree_style=ts) .. image:: im_ete3_11_0.png .. code:: ipython3 ts.layout_fn = "cluster_lines" t.render("%%inline",tree_style=ts) .. image:: im_ete3_12_0.png