R/correlationPlot.R

In eead-csic-eesa/fingerPro: Sediment Source Fingerprinting

#' Correlation matrix chart
#'
#' The function displays a correlation matrix of each of the properties divided by the different sources to help the user in the decision.
#'
#' @param data Data frame containing source and mixtures data
#' @param columns Numeric vector containing the index of the columns in the chart (the first column refers to the grouping variable)
#' @param mixtures Boolean to include or exclude the mixture samples in the chart
#' @param nmixtures Number of mixtures in the dataset
#'
#' @export
#'
correlationPlot <- function(data, columns = c(1:ncol(data)-1), mixtures = F, nmixtures = 1)  {
  # reorder the groups
  data[, 2] <- factor(data[, 2], levels = unique(data[, 2]))

  data1 <- data
  colnames(data1)[2] <- "Sources"
  if (mixtures == T) {
    # Here three mixture points are created to highlight the mixture samples in the graph
    if (nmixtures < 3) {
      data1[nrow(data1) + 1,] <- data1[nrow(data1),]
      data1[nrow(data1) + 1,] <- data1[nrow(data1),]
    ggpairs(data = data1, columns = columns+1, upper = list(continuous = "cor"), 
      lower = list(combo = "facetdensity"), title = "Correlation Matrix", 
      mapping = aes(color = Sources, alpha = 0.25), legend = c(1, 
        1)) + theme_bw() + theme(legend.position = "bottom")
    } else {
      ggpairs(data = data1, columns = columns+1, upper = list(continuous = "cor"), 
              lower = list(combo = "facetdensity"), title = "Correlation Matrix", 
              mapping = aes(color = Sources, alpha = 0.25), legend = c(1, 
              1)) + theme_bw() + theme(legend.position = "bottom")
      
    }
  } else {
    data1 <- data1[which(!data1[,2] == data1[nrow(data1),2]), ]
    ggpairs(data = data1, columns = columns+1, upper = list(continuous = "cor"), 
      lower = list(combo = "facetdensity"), title = "Correlation Matrix", 
      mapping = aes(color = Sources, alpha = 0.25), legend = c(1, 
        1)) + theme_bw() + theme(legend.position = "bottom")
  }
}