nvenn2 2.0.32

Python bindings to nVenn2 to create generalized, quasi-proportional Venn diagrams

nVennPy

This package adds a Python interface to the nVenn2 algorithm to create generalized, quasi-proportional Venn diagrams. The release version is available from Pypi by running pip install nvenn2 from an environment.

The problem

We have several sets composed of elements, like gene symbols. Each element can belong to one or more sets, which places it into a region. A region is defined by the sets it belongs to and the sets it does not belong to.

A proportional Venn diagrams shows sets inside closed lines that may intersect and define regions. The area of each region is approximately proportional to the number of elements that belong to that region. The nVenn2 algorithm is also generalized, as it can be used on any number of sets. In practice, a Venn diagram with more that six sets is difficult to interpret. However, more sets can be used if most regions are empty (see example 2).

Input

The input for nVenn2 is always a text table. The algorithm will try to guess the column separator (tab, space, comma or semicolon). Sets can be defined by row or column. If sets are in rows, the first column contains the set names. If sets are in columns, the first row contains the set names. The table is passed to the diagram() method to create a new object. The second parameter tells the module whether the sets are in columns (1) or rows (2). A value of 0 (default) tells the module to try to figure out if the sets are in rows or columns. Once the input is entered, users can also get the elements in a region with the get_venn_region method.

Simulation

After a Venn table has been loaded, the diagram is generated by calling the simulate() method on the object. Every time the method is invoked, the starting conditions change, and the result may be different. If one wants to keep a diagram, it is important to save the figure before running simulate() again.

Exhaustive simulation

If simulate() is run with a maxlevel value higher than zero, the minimization steps are performed in exhaustive mode, meaning that all combinations are tried up to the corresponding level. A maxlevel of one means that every pair switch is considered. A value of two means that all pair and two-pair switches are considered, and so forth. If maxlevel is equal to or higher than the number of regions, all possible configurations will be tested. Please, bear in mind that this process may be extremely lengthy. The computational time grows exponentially with the number of regions and with maxlevel. If you want to test this mode, you should first run estimate_exhaustive_run_time(maxlevel) to make sure that the simulation can be performed in a reasonable time.

Output

The main output of nVenn2 is an svg figure with the diagram. The svg code is obtained by calling the to_svg() method on the object. It can also be written into a file with the write_svg method. Multiple features in the figure can be customized by calling the rotate_diagram, palette, set_color, set_opacity, set_line_width, show_region_number, show_region_identifier and set_font_size methods. In addition, the diagram can be saved in the context of a web page that allows the user to explore the diagram with the to_html() method. The web page can be written to a file with the write_html method.

If a diagram is saved with the write_svg or write_html methods, the output file can be read again with the restore_from_file method.

Example 1

import nvenn2
n = nvenn2.diagram("Set1 TP53 SF3B1 POT1\nSet2 TP53 KRAS NRAS\nSet3 SF3B1 POT1 LMNA\nSet4 TP53 KRAS SF3B1", 2)
n.simulate()
print(n.tosvg())

n.get_venn_region(["Set1", "Set3"])
["POT1"]

Example 2

import nvenn2
v = nvenn2.diagram("a 1 2\nb 2 3\nc 3 4\nd 4 5\ne 5 6\nf 6 7\ng 7 8\nh 8 9\nI 9 10\nj 10 1\n", 2)

There is a public jupyter notebook hosted by Binder here.