R/data.R

In PopGenHelpR: Streamline Population Genomic and Genetic Analyses

#' A genetic differentiation matrix and locality information for each population. This data was generated
#' by subsetting data of Farleigh et al., 2021.
#'
#' A symmetric matrix with estimated genetic differentiation (Fst) between 3 populations.
#' @usage data(Fst_dat)
#' @format A list with two elements:
#' \describe{
#' \item{Fst_dat}{Data frame with three rows and three columns}
#' \item{Loc_dat}{Data frame containing the locality information for each population}
#'
#' ...
#' }
#' @examples
#' data(Fst_dat)
#' Fst <- Fst_dat[[1]]
#' Loc <- Fst_dat[[2]]
#' \donttest{
#'  Test <- Network_map(dat = Fst, pops = Loc,
#' neighbors = 2,col = c('#4575b4', '#91bfdb', '#e0f3f8','#fd8d3c','#fc4e2a'),
#' statistic = "Fst", Lat_buffer = 1, Long_buffer = 1)}
#'
#' Fstat_plot <- Pairwise_heatmap(dat = Fst, statistic = 'FST')
#'
#' @source Farleigh, K., Vladimirova, S. A., Blair, C., Bracken, J. T., Koochekian, N., Schield, D. R., ... & Jezkova, T. (2021). The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos). Molecular Ecology, 30(18), 4481-4496.
#'
"Fst_dat"
##########################################################################
#' A data frame of hypothetical heterozygosity data produced by Heterozygosity.
#'
#' Data frame containing 5 columns and 3 rows
#' @usage data(Het_dat)
#' @format A data frame with 5 columns and 3 rows:
#' \describe{
#' \item{Heterozygosity}{Estimated heterozygosity}
#' \item{Pop}{Population assignment}
#' \item{Standard.Deviation}{standard deviation}
#' \item{Longitude}{Longitude}
#' \item{Latitude}{Latitude}
#'
#' ...
#' }
#' @examples
#' \donttest{
#' data(Het_dat)
#' Test <- Point_map(Het_dat, statistic = "Heterozygosity")}
#'
#' @source Coordinates and population names taken from Farleigh, K., Vladimirova, S. A., Blair, C., Bracken, J. T., Koochekian, N., Schield, D. R., ... & Jezkova, T. (2021). The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos). Molecular Ecology, 30(18), 4481-4496.
#'
"Het_dat"
##########################################################################
#' A list representing a q-matrix and the locality information associated with the qmatrix
#'
#' List with two elements
#' @usage data(Q_dat)
#' @format A list with two elements:
#' \describe{
#' \item{Qmat}{A q-matrix with 6 columns and 30 rows, the first column lists the sample name and the remaining 5 represent the contribution a genetic cluster to that individuals ancestry}
#' \item{Loc_dat}{The locality information for each individual in the q-matrix}
#'
#' ...
#' }
#' @examples
#' \donttest{
#' data(Q_dat)
#' Qmat <- Q_dat[[1]]
#' rownames(Qmat) <- Qmat[,1]
#' Loc <- Q_dat[[2]]
#' Test_all <- Ancestry_barchart(anc.mat = Qmat, pops = Loc, K = 5,
#' plot.type = 'all',col = c('#d73027', '#fc8d59', '#e0f3f8', '#91bfdb', '#4575b4'))}
#'
#' @source Data was generated by package authors.
#'
"Q_dat"
##########################################################################
#' A population assignment data frame to be used in `Heterozygosity` and `Differentiation`.
#'
#' Data frame containing 4 columns and 72 rows
#' @usage data(HornedLizard_Pop)
#' @format A data frame with 4 columns and 72 rows:
#' \describe{
#' \item{Sample}{Sample Name}
#' \item{Population}{Population assignment according to sNMF results (see citation)}
#' \item{Longitude}{Longitude}
#' \item{Latitude}{Latitude}
#'
#' ...
#' }
#' @examples
#'  \donttest{
#' data("HornedLizard_Pop")
#' data("HornedLizard_VCF")
#' Test <- Differentiation(data = HornedLizard_VCF, pops = HornedLizard_Pop, write = FALSE)}
#'
#'
#' @source Coordinates and population names taken from Farleigh, K., Vladimirova, S. A., Blair, C., Bracken, J. T., Koochekian, N., Schield, D. R., ... & Jezkova, T. (2021). The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos). Molecular Ecology, 30(18), 4481-4496.
#'
"HornedLizard_Pop"
##########################################################################
#' A vcfR object to be used in `Heterozygosity` and `Differentiation`.
#'
#' Data frame containing 4 columns and 72 rows
#' @usage data(HornedLizard_Pop)
#' @format A vcfR object
#' \describe{
#' \item{vcfR object}{A vcfR object containing genotype and sample informaiton for 72 individuals.}
#'
#' ...
#' }
#' @examples
#'  \donttest{
#' data("HornedLizard_Pop")
#' data("HornedLizard_VCF")
#' Test <- Heterozygosity(data = HornedLizard_VCF, pops = HornedLizard_Pop, write = FALSE)}
#'
#'
#' @source Farleigh, K., Vladimirova, S. A., Blair, C., Bracken, J. T., Koochekian, N., Schield, D. R., ... & Jezkova, T. (2021). The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos). Molecular Ecology, 30(18), 4481-4496.
#'
"HornedLizard_VCF"