Plotting¶

treecat.plotting¶

treecat.plotting.add_panning_to_svg(source, destin=None)¶

Add pan and zoom to an svg file by embedding SVGPan in the file.

Args:: source: Path to the input file. destin: Path to the output file. Defaults to source.

treecat.plotting.contract_positions(XY, edges, stepsize)¶

Perturb vertex positions by an L1-minimizing attractive force.

This is used to slightly adjust vertex positions to provide a visual hint to their grouping.

Args:: XY: A [V, 2]-shaped numpy array of the current positions. edges: An [E, 2]-shaped numpy array of edges as (vertex,vertex) pairs.

treecat.plotting.layout_tree(correlation)¶

Layout tree for visualization with e.g. matplotlib.

treecat.plotting.nx_plot_tree(server, node_size=200, **options)¶

Visualize the tree using the networkx package.

This plots to the current matplotlib figure.

Args:: server: A DataServer instance. options: Options passed to networkx.draw().

treecat.plotting.plot_chord(begin, end, spacing, color, alpha=None)¶

Plots a circular chord from begin to end.

This assumes that the outer circle is centered at (0,0).

Args:: begin: A [2]-shaped numpy array. end: A [2]-shaped numpy array. spacing: A float, extra spacing around the edge of the circle. color: A matplotlib color spec. apha: A float or None.

treecat.plotting.plot_circular(server, tree_samples=0, fontsize=8, color='#4488aa', contract=0.08)¶

Plot a tree stucture with features arranged around a circle.

Args:: server: A DataServer instance. tree_samples: Number of trees to sample, in addition to the mode. fontsize: The font size for labels, in points. color: A matplotlib color spec for edge colors. contract: Contract vertex positions by this amount to visually hint

their grouping.
Requires:: matplotlib.

treecat.plotting.plot_feature_overlap(df, cmap='binary', method='cluster')¶

Plot feature-feature presence overlap of a pandas dataframe.

Args:: df: A pandas dataframe. cmap: A matplotlib colormap. method: Method of clustering, one of ‘cluster’ or ‘tree’.