In Heffley/PopGenAnalysis: Population Genomics analysis

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PopGenAnalysis

Description

PopGenAnalysis is an R package is to plot various different plots for different types of population genomic data and interpret the plots. Some of these plots include PCA plots, dendograms, and heatplots. Currently there aren't many packages that display different plots for different types of population genomic data. This package will help in doing so. This package was developed using R version 4.1.1 (2021-08-10), x86_64-w64-mingw32/x64 (64-bit)

Installation

You can install the development version of PopGenAnalysis from GitHub with:

install.packages("devtools")
devtools::install_github("Heffley/PopGenAnalysis")
library("PopGenAnalysis")

Overview

ls("package:PopGenAnalysis")

PopGenAnalysis contains 3 different functions that plot population genomics data

The pcaPopulationPlot function takes a data set of NUMERIC attributes and creates a plot to see how related the species are

The hwHeatPlot function generates the plot heatmap showing significant departures from HWE where the pink values are where p are less than or equal to alpha.

The provestiDistDendo function will display a dendogram of random n individuals/populations to visualize a genetic distance with a given data set.

browseVignettes("PopGenAnalysis")

Citation for Package

citation("PopGenAnalysis")

Chen, J. (2021) PopGenAnalysis (Different Plots for Population Genomic Data): an R package for plotting Population Genomic Data. URL https://github.com/Heffley/PopGenAnalysis

Contributions

The author of the package is Jeffrey Chen. The hwHeatPlot function uses functions from lattice pegas adegenet and dplyr. The pcaPopulationPlot uses functions from ggbiplot. The provestiDistDendo uses functions from poppr and ape.

Tutorials

For tutorials and plot interpretation, refer to the vignette:

browseVignettes("EpiGPlot")

References

Hadley Wickham, Romain François, Lionel Henry and Kirill Müller (2021). dplyr: A Grammar of Data Manipulation. R package version 1.0.7. https://CRAN.R-project.org/package=dplyr

Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24: 1403-1405. doi: 10.1093/bioinformatics/btn129

Jombart T. and Ahmed I. (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. doi: 10.1093/bioinformatics/btr521

Kamvar ZN, Tabima JF, Grünwald NJ. (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:e281. doi: 10.7717/peerj.281

Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front. Genet. 6:208. doi: 10.3389/fgene.2015.00208

Paradis E. & Schliep K. 2019. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528

Paradis E. 2010. pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26: 419-420.

Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5

Vincent Q. Vu (2011). ggbiplot: A ggplot2 based biplot. R package version 0.55. http://github.com/vqv/ggbiplot

Acknowledgements

This package was developed for BCB410H: Applied Bioinformatics, University of Toronto, Toronto, CANADA, 2021-2022. PopGenAnalysis welcomes issues, enhancement requests, and other contributions. To submit an issue, use the GitHub issues.

Heffley/PopGenAnalysis documentation built on Dec. 17, 2021, 10:32 p.m.