Skip to main content

Visualisation of PastML trees.

Project description

# cytopast

__cytopast__ is a python3 module that creates zoomable HTML visualisation of phylogenetic trees with annotated nodes.

Given a tree and its node annotations, it can either visualise them as-is,
or apply [PastML](https://github.com/saishikawa/PASTML) to infer ancestral states based on the tip states.

The states are visualised as different colours of the tree nodes using [Cytoscape.js](http://js.cytoscape.org/)

# Article

For a detailed description of PastML/cytopast: see Ishikawa SA, Zhukova A, Iwasaki W, Gascuel O (2018) __A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios__ [[bioRxiv]](https://doi.org/10.1101/379529).

# Input data
As an input, one needs to provide a **rooted** phylogenetical tree in [newick](https://en.wikipedia.org/wiki/Newick_format) format,
and a table containing tip states,
in tab-delimited (by default) or csv format (to be specified with *--data_sep ,* option).

### Example
You can download [HIV1-A in Albania data](examples/Albania/data) as an example.
Let's assume that the tree and annotation files are in the Downloads folder,
and are named respectively Albanian.tree.152tax.tre and data.txt.

The data.txt is a comma-separated file, containing tip ids in the first column,
and Country in the second column, i.e.:

id | Country
----- | -----
98CMAJ6932 | Africa
98CMAJ6933 | Africa
96CMAJ6134 | Africa
00SEAY5240 | WestEurope
... | ...
02GRAY0303 | Greece
97YUAF9960 | EastEurope

# Try it online
Try it at [pastml.pasteur.fr](https://pastml.pasteur.fr)

# Run it on your computer

There are 2 alternative ways to run cytopast on your computer: with [docker](https://www.docker.com/community-edition), or in python3.

## Run with docker

### Basic usage
Once [docker](https://www.docker.com/community-edition) is installed, run the following command:

```bash
docker run -v <path_to_the_folder_containing_the_tree_and_the_annotations>:/data:rw -t evolbioinfo/pastml --tree /data/<tree_file> --data /data/<annotation_file> --data_sep <separator_eg_comma> --columns <one_or_more_column_names> --html_compressed /data/<map_name>
```

For example, to reconstruct and visualise the ancestral Country states for Albanian data,
one needs to run the following command:

```bash
docker run -v ~/Downloads:/data:rw -t evolbioinfo/pastml --tree /data/Albanian.tree.152tax.tre --data /data/data.txt --data_sep , --columns Country --html_compressed /data/Albanian_map.html
```

This will produce a file Albanian_map.html in the Downloads folder,
that can be viewed with a browser.


### Help

To see advanced options, run
```bash
docker run -t evolbioinfo/pastml -h
```

## Run in python3

### Windows
For **Windows** users, we recommend installing cytopast via [Cygwin environment](https://www.cygwin.com/).
First instal gcc, gsl, python3 and pip3 from the Cygwin packages. Then install cytopast:
```bash
pip3 install cytopast
```

### All other platforms

We strongly recommend installing cytopast for python via [conda](https://conda.io/docs/), following the procedure described below:

#### Installing with conda

Once you have conda installed create an environment for cytopast with python3, gcc and gsl:

```bash
conda create --name cytopast python=3 gcc gsl
```

Then activate it:
```bash
source activate cytopast
```

Then install cytopast in it:

```bash
pip install cytopast
```

#### Installing without conda

Install [GNU GSL](https://www.gnu.org/software/gsl/), following the instructions provided on GSL website.

Then install cytopast:

```bash
pip3 install cytopast
```

### Basic usage in a command line
If you installed cytopast via conda, do not forget to first activate the dedicated environment, e.g.

```bash
source activate cytopast
```

To run cytopast:

```bash
cytopast --tree <path/to/tree_file.nwk> --data <path/to/annotation_file.tab> --columns <one_or_more_column_names> --html_compressed <path/to/output/map.html> --data_sep <separator_eg_comma>
```

For example, to reconstruct and visualise the ancestral Country states for Albanian data,
one needs to run the following command:

```bash
cytopast --tree ~/Downloads/Albanian.tree.152tax.tre --data ~/Downloads/data.txt --data_sep , --columns Country --html_compressed ~/Downloads/Albanian_map.html
```

This will produce a file Albanian_map.html in the Downloads folder,
that can be viewed with a browser.

### Help

To see advanced options, run:
```bash
cytopast -h
```

### Basic usage in python3
```python
from cytopast.pastml_analyser import pastml_pipeline

# Path to the table containing tip/node annotations, in csv or tab format
data = "~/Downloads/data.txt"

# Path to the tree in newick format
tree = "~/Downloads/Albanian.tree.152tax.tre"

# Columns present in the annotation table,
# for which we want to reconstruct ancestral states
# (for Albanian data we only have one column, but multiple columns are also allowed)
columns = ['Country']

# Path to the output compressed map visualisation
html_compressed = "~/Downloads/Albanian_map.html"

# (Optional) path to the output tree visualisation
html = "~/Downloads/Albanian_tree.html"

pastml_pipeline(data=data, data_sep=',', columns=columns, name_column='Country',
tree=tree,
html_compressed=html_compressed, html=html,
verbose=True)
```

### Examples

See the [examples folder](https://github.com/evolbioinfo/cytopast/tree/master/examples) for ideas :)

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
cytopast-1.1.1.tar.gz (26.8 kB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page