PR: #49 Co-authored-by: Tanguy Fardet <firstname.lastname@example.org> Co-committed-by: Tanguy Fardet <email@example.com>
Python module to plot chord diagrams with matplotlib.
Note that the repository has this structure (everything is on root level) to be able to be used more easily as a git submodule.
An example can be found in file
Here is what the diagrams look like:
- Upper left > no gradient, no gap, default colormap, chords sorted by distance
- Upper right > directed chords, no gap, "summer" colormap, rotated names, chords sorted by distance
- Lower left > gap, single color for chords, rotated names, unsorted chords
- Lower right > gradient and gap, default colormap, chords sorted by size
Main plot function
def chord_diagram(mat, names=None, order=None, sort="size", directed=False, colors=None, cmap=None, use_gradient=False, chord_colors=None, alpha=0.7, start_at=0, extent=360, width=0.1, pad=2., gap=0.03, chordwidth=0.7, min_chord_width=0, fontsize=12.8, fontcolor="k", rotate_names=False, ax=None, show=False): """ Plot a chord diagram. Draws a representation of many-to-many interactions between elements, given by an interaction matrix. The elements are represented by arcs proportional to their degree and the interactions (or fluxes) are drawn as chords joining two arcs: * for undirected chords, the size of the arc is proportional to its out-degree (or simply its degree if the matrix is fully symmetrical), i.e. the sum of the element's row. * for directed chords, the size is proportional to the total-degree, i.e. the sum of the element's row and column. Parameters ---------- mat : square matrix Flux data, ``mat[i, j]`` is the flux from i to j. names : list of str, optional (default: no names) Names of the nodes that will be displayed (must be ordered as the matrix entries). order : list, optional (default: order of the matrix entries) Order in which the arcs should be placed around the trigonometric circle. sort : str, optional (default: "size") Order in which the chords should be sorted: either None (unsorted), "size" (default, drawing largest chords first), or "distance" (drawing the chords of the two closest arcs at each end of the current arc, then progressing towards the connexions with the farthest arcs in both drections as we move towards the center of the current arc). directed : bool, optional (default: False) Whether the chords should be directed, like edges in a graph, with one part of each arc dedicated to outgoing chords and the other to incoming ones. colors : list, optional (default: from `cmap`) List of user defined colors or floats. cmap : str or colormap object (default: viridis) Colormap that will be used to color the arcs and chords by default. See `chord_colors` to use different colors for chords. use_gradient : bool, optional (default: False) Whether a gradient should be use so that chord extremities have the same color as the arc they belong to. chord_colors : str, or list of colors, optional (default: None) Specify color(s) to fill the chords differently from the arcs. When the keyword is not used, chord colors default to the colomap given by `colors`. Possible values for `chord_colors` are: * a single color (do not use an RGB tuple, use hex format instead), e.g. "red" or "#ff0000"; all chords will have this color * a list of colors, e.g. ``["red", "green", "blue"]``, one per node (in this case, RGB tuples are accepted as entries to the list). Each chord will get its color from its associated source node, or from both nodes if `use_gradient` is True. alpha : float in [0, 1], optional (default: 0.7) Opacity of the chord diagram. start_at : float, optional (default : 0) Location, in degrees, where the diagram should start on the unit circle. Default is to start at 0 degrees, i.e. (x, y) = (1, 0) or 3 o'clock), and move counter-clockwise extent : float, optional (default : 360) The angular aperture, in degrees, of the diagram. Default is to use the whole circle, i.e. 360 degrees, but in some cases it can be useful to use only a part of it. width : float, optional (default: 0.1) Width/thickness of the ideogram arc. pad : float, optional (default: 2) Distance between two neighboring ideogram arcs. Unit: degree. gap : float, optional (default: 0) Distance between the arc and the beginning of the cord. chordwidth : float, optional (default: 0.7) Position of the control points for the chords, controlling their shape. min_chord_width : float, optional (default: 0) Minimal chord width to replace small entries and zero reciprocals in the matrix. fontsize : float, optional (default: 12.8) Size of the fonts for the names. fontcolor : str or list, optional (default: black) Color of the fonts for the names. rotate_names : (list of) bool(s), optional (default: False) Whether to rotate all names (if single boolean) or some of them (if list) by 90°. ax : matplotlib axis, optional (default: new axis) Matplotlib axis where the plot should be drawn. show : bool, optional (default: False) Whether the plot should be displayed immediately via an automatic call to `plt.show()`. """
Usage and requirements
pip install mpl-chord-diagram
then, in python script or terminal:
from mpl_chord_diagram import chord_diagram
The code requires
matplotlib, which should be
installed automatically. If necessary, you can also install them by calling
pip install -r requirements.txt
Please cite our Zenodo DOI (10.5281/zenodo.6583470) if you use this library.
Libraries using mpl-chord-diagram:
- Original author: @fengwangPhysics
- Other contributors:
Alternative solutions in Python
See also the Python Graph Gallery's chord diagram entry for alternative libraries.