R/plotPCA.R

In bischrob/elemSource: Developed to source artifacts

#' Save PCA Plots
#'
#' Function to create and save PCA plots
#'
#' @param df dataframe to source
#' @param mColors optional list of colors to use in plot
#' @param showSources logical- display the sources along with the sourced artifacts
#' @param onlySources logical- only run the sources
#'
#' @return None
#'
#' @examples
#' elemSource(df)
#'
#' @export
plotPCA <- function(df,mColors, showSources = F, onlySources = F)
{ ... }

# Function
plotPCA <- function(df,mColors, showSources = F, onlySources = F){
  if(showSources == F & onlySources == T){
    stop("Cannot choose showSources = F and onlySources = T")
  }
  stopifnot(is.data.frame(df))
  artifacts <- which(df$Type == "Artifact")
  sources <- c(which(df$Type == "Source"),which(df$Type == "Source Flake"))
  if(missing(mColors)){

    myColors <- readRDS(system.file('Colors', 'Colors.Rds', package='elemSource'))
    mColors <-  myColors$Hex[1:length(unique(df$Source))]
  }
  options(warn = -1)
  suppressMessages(library(ggbiplot))
  suppressMessages(library(svDialogs))
  options(warn = 0)

  # set directory
  dName <- svDialogs::dlgDir()$res

  # PCA
  oPCAAll <- prcomp(df[,7:11], center = T, scale. = T)
  oPCAArtifacts <- prcomp(df[artifacts,7:11], center = T, scale. = T)
  oPCASources <- prcomp(df[sources,7:11], center = T, scale. = T)
  summary(oPCASources)

  # plot PCA
  if (showSources == F){
  g <- ggbiplot(oPCAArtifacts, obs.scale = 1, groups = df$Source[artifacts],
                ellipse = F, size = 2) +
    scale_color_discrete(name = '') +
    theme(legend.direction = 'horizontal',
          legend.position = 'top',
          legend.title=element_blank()) +
    scale_color_manual(values = mColors) +
    theme_bw()
  g
  ggsave(filename = paste0(dName,"/PCA Artifacts.png"),
        dpi = 300, plot = g, width = 6.5, units = "in")
  } else if (onlySources == T) {
  g <- ggbiplot(oPCASources, obs.scale = .1, groups = df$Source[sources],
              ellipse = F, size = 1, ellipse.prob = .9) +
        theme(legend.title = element_blank()) +
        scale_color_manual(values = mColors) +
        theme_bw()
  g
  ggsave(filename = paste0(dName,"/PCA Sources and Artifacts.png"),
       dpi = 300, plot = g, width = 6.5, units = "in")
  } else {
    g <- ggbiplot(oPCAAll, obs.scale = .1, groups = df$Source,
                  ellipse = F, size = 1, ellipse.prob = .9) +
      theme(legend.title = element_blank()) +
      scale_color_manual(values = mColors) +
      theme_bw()
    g
    ggsave(filename = paste0(dName,"/PCA Sources and Artifacts.png"),
           dpi = 300, plot = g, width = 6.5, units = "in")
  }
}