In Heffley/PopGenAnalysis: Population Genomics analysis
library(knitr)
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
library(PopGenAnalysis)
Introduction
PopGenAnalysis is an R package to view various different plots for different types of population genomic data such as PCA plots for data sets of populations with different numerical attributes, HWE plots, etc.
see help(package = "PopGenAnalysis") for more information and references provided by citation("PopGenAnalysis")
To download PopGenAnalysis , use the following commands:
require("devtools")
devtools::install_github("Heffley/PopGenAnalysis"，build_vignettes = TRUE)
library(PopGenAnalysis)
To list all functions available in this package:
ls("package:PopGenAnalysis")
Components
There are 3 functions in the package:
The pcaPopulationPlot allows users to input the chromosome name and gene range as arguments, then returns the summary for all transcripts within the input range, with information of gene name, transcript
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 will display a dendogram of random n individuals/populations to visualize a genetic distance with a given data set.
All the functions should be straightforward to use, as long as the valid data sets are used.
The following example illustrate how to use pcaPopulationPlot function:
pcaPopulationPlot(mtcars)
The following PCA plot should appear.
The following example illustrate how to use __*hwHeatPlot*__ function:
wzxhzdk:4
The following heatmap should appear.
The following example illustrate how to use __*provestiDistDendo*__ function:
wzxhzdk:5
A dendogram should appear, results may vary, as population is randomly picked from data set.
## Package References
[Chen, J. (2021) PopGenAnalysis (Different Plots for Population Genomic Data): an R package for
plotting Population Genomic Data.
](https://github.com/Heffley/PopGenAnalysis)
## Other 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
----
wzxhzdk:6
Heffley/PopGenAnalysis documentation built on Dec. 17, 2021, 10:32 p.m.
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library(knitr) knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(PopGenAnalysis)
Introduction
PopGenAnalysis is an R package to view various different plots for different types of population genomic data such as PCA plots for data sets of populations with different numerical attributes, HWE plots, etc.
see help(package = "PopGenAnalysis") for more information and references provided by citation("PopGenAnalysis")
To download PopGenAnalysis , use the following commands:
require("devtools") devtools::install_github("Heffley/PopGenAnalysis"，build_vignettes = TRUE) library(PopGenAnalysis)
To list all functions available in this package:
ls("package:PopGenAnalysis")
Components
There are 3 functions in the package:
The pcaPopulationPlot allows users to input the chromosome name and gene range as arguments, then returns the summary for all transcripts within the input range, with information of gene name, transcript
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 will display a dendogram of random n individuals/populations to visualize a genetic distance with a given data set.
All the functions should be straightforward to use, as long as the valid data sets are used.
The following example illustrate how to use pcaPopulationPlot function:
pcaPopulationPlot(mtcars)
The following PCA plot should appear.
The following example illustrate how to use __*hwHeatPlot*__ function:
wzxhzdk:4
The following heatmap should appear.
The following example illustrate how to use __*provestiDistDendo*__ function:
wzxhzdk:5
A dendogram should appear, results may vary, as population is randomly picked from data set.
## Package References
[Chen, J. (2021) PopGenAnalysis (Different Plots for Population Genomic Data): an R package for
plotting Population Genomic Data.
](https://github.com/Heffley/PopGenAnalysis)
## Other 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 ---- wzxhzdk:6
Heffley/PopGenAnalysis documentation built on Dec. 17, 2021, 10:32 p.m.
## Other 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 ---- wzxhzdk:6
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.