https://github.com/lkremer/cafe_fig
A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
https://github.com/lkremer/cafe_fig
cafe ete3 evolution gene-families molecular-evolution phylogenetic-trees
Last synced: 21 days ago
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A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
- Host: GitHub
- URL: https://github.com/lkremer/cafe_fig
- Owner: LKremer
- Created: 2017-06-02T11:10:39.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2019-09-05T14:11:24.000Z (over 5 years ago)
- Last Synced: 2024-03-20T04:20:38.146Z (about 1 year ago)
- Topics: cafe, ete3, evolution, gene-families, molecular-evolution, phylogenetic-trees
- Language: Python
- Homepage:
- Size: 495 KB
- Stars: 56
- Watchers: 2
- Forks: 16
- Open Issues: 10
-
Metadata Files:
- Readme: README.md
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README
CAFE_fig, a visualization tool for CAFE.
=========
[CAFE](https://hahnlab.github.io/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](https://github.com/LKremer/CAFE_fig/issues/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!](https://github.com/etetoolkit/ete/issues/354).