R/plot-gt-freq.R

In ruqianl/comapr: Crossover analysis and genetic map construction

#' plotGTFreq
#'
#' Function to plot the genotypes for all samples faceted by genotype

#' @importFrom plotly plot_ly subplot
#' @importFrom reshape2 melt
#' @inheritParams countGT
#' @author Ruqian Lyu
#' @export
#' @return A ggplot object
#' @examples
#'
#' data(snp_geno)
#' or_geno <- snp_geno[,grep("X",colnames(snp_geno))]
#' rownames(or_geno) <- paste0(snp_geno$CHR,"_",snp_geno$POS)
#' or_geno[1,] <- rep("Fail",dim(or_geno)[2])
#' cr_geno <- correctGT(or_geno,ref = snp_geno$C57BL.6J,
#'                     alt = snp_geno$FVB.NJ..i.)
#' ft_gt <- filterGT(cr_geno)
#' plotGTFreq(ft_gt)

plotGTFreq <- function(geno){

  pltdf <- data.frame(geno) %>% pivot_longer(colnames(geno),
                                                    names_to = "sample",
                                                    values_to="geno")


  stplt1 <- ggplot(data = pltdf)+
    geom_bar(mapping = aes(x = sample, fill = geno),position = "fill")+
    theme_classic(base_size = 11)+
    ylab("Genotype Frequecies for each sample")+labs(color ="Genotype")+
    theme(axis.text.x = element_text(angle =-90))

  return(stplt1)

}