R/ggbiplot.R

In cashoes/ggmixOmics: Better Graphical Outputs for `mixOmics` Models, Using `ggplot2`

#' Draws a biplot given a mixOmics plot object.
#' @author Casey Shannon
#'
#' @param model A mixOmics model object.
#' @param comps The components to visualize.
#' @param col Optional. A vector. Labels to colour points by.
#' @param ... Optional. Parameters passed to ggvarplot.
#' @import tidyverse
#' @importFrom ggrepel "geom_text_repel"
#' @importFrom ggthemes "scale_color_few"
#' @importFrom magrittr "%>%"
#' @export
ggbiplot <- function(model, ...) UseMethod('ggbiplot')

#' @rdname ggbiplot
#' @export
ggbiplot.pca <- function(model, comps = 1:2, col = NULL, ...) {
  .combine(ggcompplot(model, comps, col), ggvarplot(model, ...))
}

#' @rdname ggbiplot
#' @export
ggbiplot.DA <- function(model, comps = 1:2, ...) {
  .combine(ggcompplot(model, comps), ggvarplot(model, ...))
}

#' @rdname ggbiplot
#' @export
ggbiplot.sgccda <- function(model, comps = 1:2, ...) {
  purrr::map2(ggcompplot(model, comps), ggvarplot(model, ...), .combine)
}

# helper - rescale
.rescale <- function(x) {
  y <- sign(x)
  x <- abs(x)
  x <- (x - min(x))/(max(x) - min(x))
  x * y
}

# helper - combine plots
.combine <- function(compplot, varplot) {
  # rescale components to -1 to 1
  compplot$data <- compplot$data %>% dplyr::mutate_if(is.numeric, .rescale)
  compplot +
    ggplot2::geom_vline(xintercept = 0, alpha = 0.2) +
    ggplot2::geom_hline(yintercept = 0, alpha = 0.2) +
    ggplot2::geom_path(data = .circlefun(diameter = 1), ggplot2::aes(x, y), alpha = 0.2) +
    ggplot2::geom_path(data = .circlefun(diameter = 2), ggplot2::aes(x, y), alpha = 0.2) +
    ggrepel::geom_text_repel(data = varplot$data, ggplot2::aes(x, y, label = names), size = 2.5) +
    ggplot2::geom_segment(data = varplot$data, ggplot2::aes(x = 0, y = 0, xend = x, yend = y),
                 alpha = 0.2,
                 arrow = ggplot2::arrow(type = 'open', length = ggplot2::unit(0.25,"cm")))
}