README.md

In RomainFeron/radsex-vis: Visualization of results from the RADSex pipeline

radsex-vis

The radsex-vis R package is currently under development and has not been officially released yet. Missing features are been implemented, and some bugs are to be expected in this current development version. Please contact me by email or on Github, or open an issue if you encounter bugs or would like to discuss a feature !

Overview

The radsex-vis R package was developed to visualize results from the RADsex pipeline. For each RADSex command, there is a corresponding function in radsex-vis to easily generate a plot from the results file of RADSex. For each analysis, the general organisation of radsex-vis is as follows:

• A function to directly plot the results file, for instance, plot_sex_distribution(). This is the function you should use most of the time, and its name always starts with plot.
• A function to load data from a specific results file, for instance load_sex_distribution_table(). This function's name always starts with load.
• A function to generate a plot from a results file loaded in R, for instance sex_distribution_heatmap().

The plot functions are meant to be easy to use while still offering in-depth customization if desired. Other functions can be used by experienced R users who would like more control over the plotting steps.

This package was developed in the LPGP lab from INRA, Rennes, France for the PhyloSex project, which investigates sex determining factors in a wide range of fish species.

Requirements

• The package was developed and tested in R version 3.4.4.

Installation

We may try to get radsex-vis on CRAN in the future; in the meantime, radsex-vis can be installed with devtools by using the following commands in R:

install.packages("devtools")
library(devtools)
devtools::install_github("INRA-LPGP/radsex-vis")

Quick guide

All functions are documented and the detailed usage for each function is available in R with ?function_name, for instance ?plot_sex_distribution (or ?radsexvis::plot_sex_distribution if the package was not loaded). Below is a summary of the main functions:

Function | Description ----------------------- | ------------ plot_sex_distribution | Generates a sex distribution heatmap from the results of RADSex distrib plot_coverage | Generates a coverage heatmap from the results of RADSex subset, signif, or loci. plot_genome | Generates a whole genome circular plot from the results of RADSex map. plot_scaffold | Generates a linear plot for the specified scaffold from the results of RADSex map.

Examples of results

Sex distribution

Coverage

Whole genome mapping

Scaffold mapping

LICENSE

Copyright (C) 2018 Romain Feron and INRA LPGP

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/

RomainFeron/radsex-vis documentation built on May 23, 2019, 2:48 p.m.