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/)
## Installation
```bash
pip3 install cytopast
```
## 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 = "/path/to/the/table/eg/data.csv"
# Path to the tree in newick format
tree = "/path/to/the/tree/eg/tree.nwk"
# Columns present in the annotation table,
# for which we want to reconstruct ancestral states
columns = ['Location', 'Resistant_or_not']
# Columns present in the annotation table,
# for which we want to copy existing annotations from the annotation table,
# without inferring ancestral states
copy_columns = ['Sex']
# Path to the output compressed map visualisation
html_compressed = "/path/to/the/future/map/eg/map.html"
# Path to the output tree visualisation
html = "/path/to/the/future/tree/visualisation/eg/tree.html"
pastml_pipeline(data=data, data_sep=',', columns=columns, name_column='Location',
tree=tree,
html_compressed=html_compressed, html=html,
verbose=True)
```
## Options
```
usage: pastml_analyser.py [-h] --data DATA [--data_sep DATA_SEP]
[--id_index ID_INDEX]
[--columns [COLUMNS [COLUMNS ...]]]
[--copy_columns [COPY_COLUMNS [COPY_COLUMNS ...]]]
--tree TREE [--model MODEL] [--work_dir WORK_DIR]
[--cache] [--name_column NAME_COLUMN] [--all]
[--out_data OUT_DATA]
[--html_compressed HTML_COMPRESSED] [--html HTML]
[--verbose]
Visualisation of annotated phylogenetic trees (as html maps).
optional arguments:
-h, --help show this help message and exit
--verbose print information on the progress of the analysis
annotation-related arguments:
--data DATA the annotation file in tab/csv format with the first
row containing the column names.
--data_sep DATA_SEP the column separator for the data table. By default is
set to tab, i.e. for tab file. Set it to ',' if your
file is csv.
--id_index ID_INDEX the index of the column in the data table that
contains the tree tip names, indices start from zero
(by default is set to 0).
--columns [COLUMNS [COLUMNS ...]]
names of the data table columns that contain states to
be analysed with PASTML. If neither columns nor
copy_columns are specified, then all columns will be
considered for PASTMl analysis.
--copy_columns [COPY_COLUMNS [COPY_COLUMNS ...]]
names of the data table columns that contain states to
be copied as-is, without applying PASTML (the missing
states will stay unresolved).
tree-related arguments:
--tree TREE the input tree in newick format.
ancestral-state inference-related arguments:
--model MODEL the evolutionary model to be used by PASTML (can be JC
or F81).
--work_dir WORK_DIR the working dir for PASTML to put intermediate files
into (if not specified a temporary dir will be
created).
--cache if set, the results of previous PASTML runs on this
data will be reused when possible
visualisation-related arguments:
--name_column NAME_COLUMN
name of the data table column to be used for node
names in the compressed map visualisation(must be one
of those specified in columns or copy_columns if they
are specified).If the data table contains only one
column it will be used by default.
--all Keep all the nodes in the compressed map
visualisation, even the minor ones.
output-related arguments:
--out_data OUT_DATA the output annotation file with the states inferred by
PASTML.
--html_compressed HTML_COMPRESSED
the output summary map visualisation file (html).
--html HTML the output tree visualisation file (html).
```
__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/)
## Installation
```bash
pip3 install cytopast
```
## 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 = "/path/to/the/table/eg/data.csv"
# Path to the tree in newick format
tree = "/path/to/the/tree/eg/tree.nwk"
# Columns present in the annotation table,
# for which we want to reconstruct ancestral states
columns = ['Location', 'Resistant_or_not']
# Columns present in the annotation table,
# for which we want to copy existing annotations from the annotation table,
# without inferring ancestral states
copy_columns = ['Sex']
# Path to the output compressed map visualisation
html_compressed = "/path/to/the/future/map/eg/map.html"
# Path to the output tree visualisation
html = "/path/to/the/future/tree/visualisation/eg/tree.html"
pastml_pipeline(data=data, data_sep=',', columns=columns, name_column='Location',
tree=tree,
html_compressed=html_compressed, html=html,
verbose=True)
```
## Options
```
usage: pastml_analyser.py [-h] --data DATA [--data_sep DATA_SEP]
[--id_index ID_INDEX]
[--columns [COLUMNS [COLUMNS ...]]]
[--copy_columns [COPY_COLUMNS [COPY_COLUMNS ...]]]
--tree TREE [--model MODEL] [--work_dir WORK_DIR]
[--cache] [--name_column NAME_COLUMN] [--all]
[--out_data OUT_DATA]
[--html_compressed HTML_COMPRESSED] [--html HTML]
[--verbose]
Visualisation of annotated phylogenetic trees (as html maps).
optional arguments:
-h, --help show this help message and exit
--verbose print information on the progress of the analysis
annotation-related arguments:
--data DATA the annotation file in tab/csv format with the first
row containing the column names.
--data_sep DATA_SEP the column separator for the data table. By default is
set to tab, i.e. for tab file. Set it to ',' if your
file is csv.
--id_index ID_INDEX the index of the column in the data table that
contains the tree tip names, indices start from zero
(by default is set to 0).
--columns [COLUMNS [COLUMNS ...]]
names of the data table columns that contain states to
be analysed with PASTML. If neither columns nor
copy_columns are specified, then all columns will be
considered for PASTMl analysis.
--copy_columns [COPY_COLUMNS [COPY_COLUMNS ...]]
names of the data table columns that contain states to
be copied as-is, without applying PASTML (the missing
states will stay unresolved).
tree-related arguments:
--tree TREE the input tree in newick format.
ancestral-state inference-related arguments:
--model MODEL the evolutionary model to be used by PASTML (can be JC
or F81).
--work_dir WORK_DIR the working dir for PASTML to put intermediate files
into (if not specified a temporary dir will be
created).
--cache if set, the results of previous PASTML runs on this
data will be reused when possible
visualisation-related arguments:
--name_column NAME_COLUMN
name of the data table column to be used for node
names in the compressed map visualisation(must be one
of those specified in columns or copy_columns if they
are specified).If the data table contains only one
column it will be used by default.
--all Keep all the nodes in the compressed map
visualisation, even the minor ones.
output-related arguments:
--out_data OUT_DATA the output annotation file with the states inferred by
PASTML.
--html_compressed HTML_COMPRESSED
the output summary map visualisation file (html).
--html HTML the output tree visualisation file (html).
```
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