:orphan:

Gallery
=======
.. warning::
  If plots do not show on screen, try adding `show=True` to your function call:

  .. code-block::

    ipx.network(
      ...,
      show=True,
    )

  This is a peculiarity of `matplotlib`_, the plotting engine behind `iplotx`,
  and depends on your Python environment (e.g., Jupyter notebooks, terminal,
  interactive mode, backend, etc). You might want to enable `interactive mode`_
  *before* plotting to ensure everything is rendered immediately:

  .. code-block::

    import matplotlib.pyplot as plt
    import iplotx as ipx

    ...

    plt.ion()
    ipx.network(
      ...,
    )

  If interactive mode is on, you do not need `show=True` (because plots are
  always rendered immediately anyway).

.. _matplotlib: https://matplotlib.org/
.. _interactive mode: https://matplotlib.org/stable/users/explain/figure/interactive.html



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. thumbnail-parent-div-close

.. raw:: html

    </div>

Basic
+++++



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to plot a simple graph with iplotx.">

.. only:: html

  .. image:: /gallery/basic/images/thumb/sphx_glr_plot_basic_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_basic_plot_basic.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Basic network plotting</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to plot a simple graph with iplotx.">

.. only:: html

  .. image:: /gallery/basic/images/thumb/sphx_glr_plot_directed_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_basic_plot_directed.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Simple directed graph</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example showcases the ability of iplotx to curve edges at a certain tension setting.">

.. only:: html

  .. image:: /gallery/basic/images/thumb/sphx_glr_plot_big_curves_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_basic_plot_big_curves.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Big curves</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="A minimal example of using iplotx together with networkx.">

.. only:: html

  .. image:: /gallery/basic/images/thumb/sphx_glr_plot_simple_path_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_basic_plot_simple_path.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Simple path</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example showcases the ability of iplotx to curve edges into arcs, using tension to define the angular span of the arc.">

.. only:: html

  .. image:: /gallery/basic/images/thumb/sphx_glr_plot_arcs_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_basic_plot_arcs.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Arcs</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to visualise graphs or networks in 3D using iplotx. Of course, a 3D layout is needed for this. Here, we use the Fruchterman-Reingold layout algorithm from igraph to generate a 3D layout.">

.. only:: html

  .. image:: /gallery/basic/images/thumb/sphx_glr_plot_3d_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_basic_plot_3d.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">3D layouts</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to create a random directed acyclic graph (DAG) and how to use igraph layouts based on strings.">

.. only:: html

  .. image:: /gallery/basic/images/thumb/sphx_glr_plot_dag_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_basic_plot_dag.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Directed Acyclic Graph</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from networkx shows how to integrate network attributes/data and plotting.">

.. only:: html

  .. image:: /gallery/basic/images/thumb/sphx_glr_plot_house_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_basic_plot_house.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Plot a house</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use the grouping argument to visualise vertex covers or clustering, including singletons (i.e. groups of one vertex).">

.. only:: html

  .. image:: /gallery/basic/images/thumb/sphx_glr_plot_grouping_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_basic_plot_grouping.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Grouping</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This minimal example shows how to style a plot loops.">

.. only:: html

  .. image:: /gallery/basic/images/thumb/sphx_glr_plot_loops_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_basic_plot_loops.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Loops</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>

Biology and Ecology
+++++++++++++++++++



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example visualises network of putatively interacting proteins according to the STRING database, filtered to include only entries related to breast cancer.">

.. only:: html

  .. image:: /gallery/biology/images/thumb/sphx_glr_plot_breast_cancer_ppi_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_biology_plot_breast_cancer_ppi.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Breast cancer proteins</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to visualise Protein Protein Interaction (PPI) networks using iplotx.">

.. only:: html

  .. image:: /gallery/biology/images/thumb/sphx_glr_plot_ppi_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_biology_plot_ppi.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Protein Protein Interactions</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from cogent3 shows how to use iplotx to visualise a phylogenetic tree of many animals.">

.. only:: html

  .. image:: /gallery/biology/images/thumb/sphx_glr_plot_animal_phylogeny_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_biology_plot_animal_phylogeny.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Animal phylogeny</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to visualise the bipartite relationship between plants and their pollinators using iplotx.">

.. only:: html

  .. image:: /gallery/biology/images/thumb/sphx_glr_plot_pollinators_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_biology_plot_pollinators.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Pollinators</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example visualises protein protein interactions involved in the &quot;cell cycle arrest&quot; pathway.">

.. only:: html

  .. image:: /gallery/biology/images/thumb/sphx_glr_plot_cell_cycle_arrest_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_biology_plot_cell_cycle_arrest.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Cell cycle arrest</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example visualises a subset of the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle or citric acid cycle.">

.. only:: html

  .. image:: /gallery/biology/images/thumb/sphx_glr_plot_tca_cycle_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_biology_plot_tca_cycle.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">TCA cycle</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to visualise the antibodies of a large repertoire clone with iplotx.">

.. only:: html

  .. image:: /gallery/biology/images/thumb/sphx_glr_plot_antibody_clone_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_biology_plot_antibody_clone.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Antibody clones</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example visualises a table of foraging strategies, as found at https://doi.org/10.1111/1365-2656.13609.">

.. only:: html

  .. image:: /gallery/biology/images/thumb/sphx_glr_plot_foraging_table_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_biology_plot_foraging_table.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Foraging table</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example visualises a food network, with data taken from https://doi.org/10.3389/fevo.2020.588430 (Supplementary Table S1).">

.. only:: html

  .. image:: /gallery/biology/images/thumb/sphx_glr_plot_food_network_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_biology_plot_food_network.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Food network</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>

Fun
+++



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows that yo 6-7.">

.. only:: html

  .. image:: /gallery/fun/images/thumb/sphx_glr_plot_67_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_fun_plot_67.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">6-7</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to visualise train tracks using iplotx. The layout, ports, edges, and colors are crafted by hand, as you would expect for such a bespoke diagram.">

.. only:: html

  .. image:: /gallery/fun/images/thumb/sphx_glr_plot_train_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_fun_plot_train.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Train tracks</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>

Network science
+++++++++++++++



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="The same graph in igraph and networkx, plotted with iplotx.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_parallel_igraph_networkx_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_parallel_igraph_networkx.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">igraph/networkx compatibility</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to use iplotx with networkx. Note how the vertex size is computed dynamically based on label size.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_simple_networkx_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_simple_networkx.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Simple example from networkx</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from networkx shows how to use simple vertex styling.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_multipartite_layout_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_multipartite_layout.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Multipartite layout</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from networkx shows how to use complex network properties including edge tension.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_complex_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_complex.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Complex example</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from networkx shows how to use edge labels and their rotation.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_shortest_path_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_shortest_path.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Shortest path</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to visualise simple logical relationships, for instance the organisational chart of a company.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_company_structure_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_company_structure.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Company structure</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example inspired by SocNetV (https://socnetv.org/data/uploads/screenshots/32/socnetv-32-example-dot.png), shows social connections within circles. It also demonstrates how to combine iplotx with other matplotlib artists.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_social_network_circles_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_social_network_circles.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Social circles</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from igraph shows how to work with edge labels and linewidths.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_minimum_spanning_trees_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_minimum_spanning_trees.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Minimum spanning trees</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from networkx demonstrates simple styling of nodes and edges.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_traveling_salesman_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_traveling_salesman.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Traveling salesman</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from networkx demonstrates how to use transparency to overlay multiple plots with distinct highlights.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_labels_and_colors_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_labels_and_colors.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Labels and colors</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to overlay an iplotx artist with plain matplotlib patches.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_redblack_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_redblack.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">The red and the black</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from igraph presents how to visualise bipartite matching using maximum flow, with edge linewidth and vertex facecolor styling.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_max_bipartite_matching_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_max_bipartite_matching.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Maximum Bipartite Matching by Maximum Flow</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates the visualisation of a network with 1,000 nodes and a few thousand edges, using a custom layout that resembles a lawn of arrows.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_arrowlawn_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_arrowlawn.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Arrow lawn</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from igraph shows how to compute and visualize cliques and highlight them.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_cliques_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_cliques.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Cliques</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from newtorkx shows an undirected graph of 128 US cities.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_knuth_miles_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_knuth_miles.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Knuth Miles US cities</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from networkx shows how to use mappable colors and colormaps and how to connect them to a colorbar.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_with_colorbar_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_with_colorbar.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Colorbar</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from networkx shows how to use coloring and custom layout as a dictionary.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_cluster_layout_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_cluster_layout.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Cluster of Southern Women</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from networkx shows the relatinoships between chess masters. The example has a lot of network analysis code that is somewhat irrelevant for iplotx and is kept to demonstrate functional parity.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_chess_masters_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_chess_masters.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Chess masters</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates the use of iplotx to visualise financial relationships, mimicking a figure published in this paper: https://www.science.org/doi/10.1126/science.1173644.">

.. only:: html

  .. image:: /gallery/network_science/images/thumb/sphx_glr_plot_financial_network_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_network_science_plot_financial_network.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Financial network</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>

Other
+++++



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to plot a bunch of arcs.">

.. only:: html

  .. image:: /gallery/other/images/thumb/sphx_glr_plot_multiarc_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_other_plot_multiarc.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Multiarc</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to plot edge strings around a circle.">

.. only:: html

  .. image:: /gallery/other/images/thumb/sphx_glr_plot_bundles_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_other_plot_bundles.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Edge strings</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Graphs with arrows and bars are commonly used to represent feedback loops in systems. This example shows how to obtain that effect in iplotx.">

.. only:: html

  .. image:: /gallery/other/images/thumb/sphx_glr_plot_feedbacks_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_other_plot_feedbacks.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Feedback loops</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="One of the strengths of iplotx is the support for editing artists after they have been plotted the first time without making a whole new figure.">

.. only:: html

  .. image:: /gallery/other/images/thumb/sphx_glr_plot_edit_artists_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_other_plot_edit_artists.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Editing artists after plotting</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to display changes of a quantity over time. This is a kind of chart that would not usually be considered a graph, but can be reinterpreted that way to make use of iplotx&#x27;s visual capabilities.">

.. only:: html

  .. image:: /gallery/other/images/thumb/sphx_glr_plot_graph_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_other_plot_graph.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Charts as graph visualisations</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to interact with mouse events (e.g. hovering) in iplotx.">

.. only:: html

  .. image:: /gallery/other/images/thumb/sphx_glr_plot_mouse_hover_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_other_plot_mouse_hover.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Mouse event handling</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx with cartopy for geodata.">

.. only:: html

  .. image:: /gallery/other/images/thumb/sphx_glr_plot_geomap_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_other_plot_geomap.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Aftican cities</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial shows how to animate iplotx visualizations using matplotlib.animation.FuncAnimation.">

.. only:: html

  .. image:: /gallery/other/images/thumb/sphx_glr_plot_animation_thumb.gif
    :alt:

  :ref:`sphx_glr_gallery_other_plot_animation.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Animations</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to highlight a node and its neighborhood by hovering with the mouse on it.">

.. only:: html

  .. image:: /gallery/other/images/thumb/sphx_glr_plot_hover_neighborhood_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_other_plot_hover_neighborhood.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Hover neighborhoods</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot constellations. Data comes from Wikipedia: https://en.wikipedia.org/wiki/List_of_stars_in_Draco.">

.. only:: html

  .. image:: /gallery/other/images/thumb/sphx_glr_plot_constellation_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_other_plot_constellation.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Constellation</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>

Style
+++++



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows to to use depth shading in 3D plots to reduce the opacity (increase transparency) of vertices and edges that are further away from the viewer. This gives a better sense of depth but can be confusing in some cases, so there are style options to turn it off.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_depthshade_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_depthshade.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">3D depth shading</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Sometimes the need arises to color edges with multiple colors at the same time. That&#x27;s what multigraphs are for. This example shows the concept in action.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_edge_multicolor_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_edge_multicolor.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Multicolor edges</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Most of the time edges have no &quot;filling&quot;, but what if they did? Then you would get this crazy example.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_filled_edges_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_filled_edges.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Filled edges</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates the use of edge waypoints.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_waypoints_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_waypoints.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Edge waypoints</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example illustrates how to shrink edges, i.e. leave a bit of empty space between edge cap (end) and the border of its source/target vertices.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_edgepadding_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_edgepadding.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Edge shrink</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates the use of curved edge waypoints. For straight waypoints, the edge will pass through each waypoint. For curved waypoints, they are used as cubic Bezier points to interpolate smoothly between.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_curved_waypoints_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_curved_waypoints.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Curved waypoints</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a few simple styling options available in iplotx.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_style_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_style.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Basics of styling</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example showcases various types of arrowheads for connected graphs.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_arrows_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_arrows.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Arrowheads</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows various kinds of vertex markers that can be used in iplotx.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_vertexmarkers_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_vertexmarkers.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Vertex markers</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrated the use of half arrows for directed graphs.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_halfarrows_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_halfarrows.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Half arrows</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows the same network plotted with a variery of styles from the iplotx style library.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_multistyle_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_multistyle.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Style library</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example showcases various plot elements that can be styled in iplotx.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_elements_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_elements.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Network element showroom</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to use ports, which specify at which angle edges exit from and enter into vertices.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_ports_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_ports.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Edge ports</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to combine iplotx visualisations with other tools such as scipy and vanilla matplotlib. This is one of the key strengths of iplotx over custom visualisations in many other packages: iplotx produces fully compliant matplotlib artists that can be combined with other matplotlib tools, including seaborn.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_voronoi_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_voronoi.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Voronoi tessellation</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use edge geometries and tension to achieve different visualisation styles.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_edge_geometries_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_edge_geometries.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Edge geometries</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use edge tension to create curved edges with sharper turns.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_tension_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_tension.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Edge tension</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example from networkx shows different stylings for the same grid.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_four_grids_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_four_grids.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Four grids</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use a custom vertex shape in an iplotx graph. These can be polygons, i.e. instances of matplotlib.patches.Polygon, or more general paths, i.e. instances of matplotlib.path.Path.">

.. only:: html

  .. image:: /gallery/style/images/thumb/sphx_glr_plot_custom_vertex_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_style_plot_custom_vertex.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Custom vertex shape</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>

Trees
+++++



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to add a scale bar to an iplotx tree.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_scalebar_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_scalebar.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Scale bar</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example showcases the &quot;equal angle&quot; layout. This layout is inspired by the ggtree layout with the same name, which originally comes from Joseph Felsenstein&#x27;s book &quot;Inferring Phylogenies&quot;.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_equalangle_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_equalangle.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Equal angle layout</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot trees from skbio or scikit-bio.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_skbio_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_skbio_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">scikit-bio tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use leaf edges, dashed lines connecting each leaf to the deepest leaf and label.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_leafedges_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_leafedges.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Leaf edges</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This Biopython-inspired example shows how to style clade edges for a node and its descendants.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_cladeedges_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_cladeedges.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Subtrees and cascades</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This short example demonstrates how to combine leaf edges and cascades.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_leafedges_and_cascades_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_leafedges_and_cascades.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Leaf edges and cascades</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use split edges, i.e. how to apply different styles to tree edges that are composed of multiple segments. See also ../zero_dependency/plot_simpletreedataprovider for the basic example of how to plot a tree with iplotx&#x27;s internal tree representation.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_split_edges_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_split_edges.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Split edges</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows a few elements from  iplotx&#x27;s style hierarchy.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_style_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_style_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Style hierarchy</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot trees from cogent3, the successor to pycogent.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_cogent3_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_cogent3_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Cogent3 tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to style tree clades - or subtrees - post rendering, similar of the equivalent option in cogent3.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_tree_style_clades_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_tree_style_clades.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Subtree styling</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to visualise support values for clades or branches.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_support_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_support.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Branch support</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot trees from dendropy.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_dendropy_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_dendropy.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Dendropy tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot trees from Biopython&#x27;s Phylo module.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_biopython_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_biopython_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Biopython tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot trees from ete4.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_ete4_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_ete4.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">ETE4 tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates iplotx&#x27;s capability to style tree appearance with an angular look, either for the whole tree or specific edges.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_angular_waypoints_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_angular_waypoints.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Angular layout and edge waypoints</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to reproduce cogent3 layouts using iplotx.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_cogent3_layouts_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_cogent3_layouts.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Cogent3 layouts</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example showcases plot elements for tree styling in iplotx.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_elements_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_elements_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Tree element showroom</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to plot two trees facing each other, which is typical in coevolutionary studies.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_double_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_double_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Double tree</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to plot trees at the leaf of a tree, using the iplotx library. Note that there are a few conceivable ways to do similar things as this in matplotlib and this is just one such approach, using inset axes.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_trees_of_trees_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_trees_of_trees.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Tree of trees</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to use iplotx to add cascading backgrounds to trees. &quot;Cascading&quot; here means that each patch (rectangle/wedge/etc.) will cover a node and all descendants, down to the leaves.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_tree_node_background_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_tree_node_background.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Tree cascades</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to plot trees from the phyloframe library, using Seaborn to overlay scatter points.">

.. only:: html

  .. image:: /gallery/tree/images/thumb/sphx_glr_plot_phyloframe_tree_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_tree_plot_phyloframe_tree.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">phyloframe tree</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>

Zero-dependency
+++++++++++++++



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example uses iplotx&#x27;s internal SimpleNetworkDataProvider to show how to visualise networkx without using any external analysis library (e.g. igraph, networkx).">

.. only:: html

  .. image:: /gallery/zero_dependency/images/thumb/sphx_glr_plot_simplenetworkdataprovider_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_zero_dependency_plot_simplenetworkdataprovider.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Zero-dependency networks</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to visualise trees using iplotx&#x27;s internal SimpleTree, a simple tree representation via the children attribute.">

.. only:: html

  .. image:: /gallery/zero_dependency/images/thumb/sphx_glr_plot_simpletreedataprovider_thumb.png
    :alt:

  :ref:`sphx_glr_gallery_zero_dependency_plot_simpletreedataprovider.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Zero-dependency trees</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>


.. toctree::
   :hidden:
   :includehidden:


   /./gallery/basic/index.rst
   /./gallery/biology/index.rst
   /./gallery/fun/index.rst
   /./gallery/network_science/index.rst
   /./gallery/other/index.rst
   /./gallery/style/index.rst
   /./gallery/tree/index.rst
   /./gallery/zero_dependency/index.rst


.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-gallery

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download all examples in Python source code: gallery_python.zip </gallery/gallery_python.zip>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download all examples in Jupyter notebooks: gallery_jupyter.zip </gallery/gallery_jupyter.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_