CAFE_fig, a visualization tool for CAFE.

CAFE (Computational Analysis of gene Family Evolution) is a software that provides a statistical foundation for evolutionary inferences about changes in gene family size.

The visualization and interpretation of CAFE results usually requires custom scripts. Here, I provide such a custom script.

CAFE_fig takes a .cafe output file and produces:

• a summary tree that shows the average expansion/contraction of families across the phylogeny
• a tree that denotes which branches evolve under which lambda (if a model with multiple lambdas was used)
• a tree for each family of interest, i.e. families that the user specified by ID or families that showed significant change at a user-specified clade of interest

Requirements

CAFE_fig requires Python3.4+ and ETE3: Install ETE3 with

pip3 install 'ete3==3.0.0b35'

It's important that you use ETE3 version 3.0.0b35 since it appears that the latest ETE3 version causes problems that are beyond my control (see issue #1). This ETE3 version runs well with PyQt4 but not PyQt5, so if you're experiencing issues it's worth a try to switch to PyQt4.

Usage

usage: CAFE_fig.py [-h] [-f FAMILIES [FAMILIES ...]] [-c CLADES [CLADES ...]]
                   [-pb PB] [-pf PF] [-d DUMP] [-g GFX_OUTPUT_FORMAT]
                   [--count_all_expansions]
                   report_cafe

Parses a CAFE output file (.cafe) and plots a summary tree that shows the
average expansion/contraction across the phylogeny; a tree that shows which
clades evolved under the same lambda (if available); and a gene family
evolution tree for each user-specified gene family.

positional arguments:
  report_cafe           the file report.cafe (or similar name)

optional arguments:
  -h, --help            show this help message and exit
  -f FAMILIES [FAMILIES ...], --families FAMILIES [FAMILIES ...]
                        only show families with these IDs
  -c CLADES [CLADES ...], --clades CLADES [CLADES ...]
                        only show families that are expanded/contracted at
                        this clade. Format: [clade]=[leaf],[leaf] where clade
                        is the name of the last common ancestor of the two
                        leaves, e.g.: Isoptera=zne,mna
  -pb PB                branch p-value cutoff (default: 0.05)
  -pf PF                family p-value cutoff (default: 0.05)
  -d DUMP, --dump DUMP  don't open trees in a window, write them to files in
                        the specified directory instead (default: off)
  -g GFX_OUTPUT_FORMAT, --gfx_output_format GFX_OUTPUT_FORMAT
                        output format for the tree figures when using --dump
                        [svg|pdf|png] (default: pdf)
  --count_all_expansions
                        count and write down the number of *all* expansions
                        and contractions (default: only count significant
                        expansions/contractions)

Example outputs

Summary tree that shows the average expansion/contraction (radius of node circles), the numbers of expanded/contracted families (+/-), and the estimated gene gain/loss rates (blue: low rate; red: high rate).

Example output for a specific gene family. Numbers and node sizes represent the family size at each node. Significant expansions are shown in green, significant contractions in magenta.

Example usage

To recreate the plots shown above, use this command:

python3 ./CAFE_fig.py example_result.cafe -c Isoptera=zne,mna -pb 0.05 -pf 0.05 --dump test/ -g .pdf --count_all_expansions

This reads "example_result.cafe" and dumps all figures in PDF format to the directory "test/". The summary tree ("summary.pdf") will show the whole phylogeny and the number of expansions and contractions (including insignificant ones!) as shown below. Further family-wise trees will be created and dumped in the directory "test/families". These trees will only be created for families that showed a significant (p<=0.05) expansion/contraction at the node "Isoptera", which is the last common ancestor of "zne" and "mna".

Significant contractions are marked in magenta, significant expansions are marked in green (p<=0.001 = ***, p<=0.01 = **, p<=0.05 = *).

Known issues

The error message module 'ete3' has no attribute 'TreeStyle' is caused by a known problem with ete3 that is beyond my control. Check this link for possible solutions!.