https://github.com/stuntspt/misc_plotters
A collection of scripts for plotting several kinds of data
https://github.com/stuntspt/misc_plotters
Last synced: 2 months ago
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A collection of scripts for plotting several kinds of data
- Host: GitHub
- URL: https://github.com/stuntspt/misc_plotters
- Owner: StuntsPT
- License: gpl-3.0
- Created: 2015-03-18T15:20:40.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2016-11-11T22:05:24.000Z (over 9 years ago)
- Last Synced: 2025-01-17T20:45:34.631Z (about 1 year ago)
- Language: Python
- Size: 109 KB
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# misc_plotters
A collection of scripts for plotting several kinds of data.
Some examples of what these scripts produce can be found in the "examples" directory.
-------
## Fst_heatmap.R
This is a dirty script (it's all hardcoded, and uses non-conventional files) to draw the two parts of a Fst plot.
### Input files
The data utilized in this script can be obtained with [Genepop](http://kimura.univ-montp2.fr/~rousset/), in the output.MIG
The first part requires a triangular matrix (upper and lower) of pairwise Fst values. Eg.:
A B C D
A 0 2 2 2
B 1 0 2 2
C 1 1 0 2
D 1 1 1 0
Where the 1's are the pairwise Fst values from one dataset and the 2's are for a different dataset. The diagonal must be filled with 0's.
For the second part (the line plots) you will require a file with Fst values for each dataset (one value per line). Eg.:
1
1
1
1
1
To use the script, just replace the hard-coded paths with the path to your own files.
### Requirements
This script requires the "corrplot" package. You can download it from CRAN.
-------
## Mantel_plotter.R
This script will plot the data used for a Mantel test and the associates correlation line.
Does not give a very nice result. It has been abandoned before being really useful.
Still full hard-coded.
--------
## Correlogram.R
This script will grab 2 triangular matrices (generated with GenePop), one genetic distance and one of geographic distance and will plot the respective Mantel correlograms.
Fully hard coded.
---------
## map_plotter.R
This script will plot a measurement of genetic diversity (or any value as for that matter) in a coordinate system, along with the interpolation between each data point.
Hard coded and poorly documented (but the code should be simple enough to understand). Use at your own risk.
--------
## Allele_freq_plotter.py
Not yet documented. Sorry for any inconvenience.
## p-value-freqs.py
This script will parse a single column file with one p-value (or q-value) per line and plot a frequency histogram.
Requirements and usage can be found within the script itself.
## License
GPLv3