R/skewnorm.contour.R

In Compositional: Compositional Data Analysis

 ################################
#### Contour plot of the bivariate skew normal distribution in S^2
#### Tsagris Michail 2/2013
#### mtsagris@yahoo.gr
#### References: Azzalini A. and Valle A. D. (1996).
#### The multivariate skew-normal distribution. Biometrika 83(4):715-726.
skewnorm.contour <- function(x, type = 'alr', n = 100, appear = TRUE, cont.line = FALSE) {
  ## the type parameter determines whether the additive
  ## or the isometric log-ratio transformation will be used.
  ## If type='alr' (the default) the additive log-ratio transformation is used.
  ## If type='ilr', the isometric log-ratio is used
  ## n is the number of points of each axis used
  nam <- c("X1", "X2", "X3")
  x1 <- seq(0.001, 0.999, length = n)
  sqrt3 <- sqrt(3)
  x2 <- seq(0.001, sqrt3/2 - 0.001, length = n)

  if (type == "alr") {
    y <- Compositional::alr(x) # additive log-ratio transformation
  } else y <- Compositional::alfa(x, 0)$aff

  mod <- sn::msn.mle(y = y)
  param <- mod$dp
  y <- NULL

  wa <- NULL
  for ( i in 1:n ) {
    w3 <- 2 * x2 / sqrt3
    w2 <- x1[i] - x2/sqrt3
    w1 <- 1 - w2 - w3
    wa <- rbind(wa, cbind(w1, w2, w3) )
  }

  if (type == "alr") {
    y <- Compositional::alr(wa) # additive log-ratio transformation
  } else y <- Compositional::alfa(wa, 0)$aff

  can <- sn::dmsn(y, dp = param)
  mat <- matrix(can, byrow = TRUE, nrow = n, ncol = n)

 # Create triangle corners
  b1 <- c(0.5, 0, 1, 0.5)

  b2 <- c(sqrt3/2, 0, 0, sqrt3/2)
  b <- cbind(b1, b2)

# Axes
b_x1 <- seq(from = 0, to = 1, length.out = 11)
b_y1 <- rep(0, times = 11)

b_x2 <- seq(from = 0.5, to = 0, length.out = 11)
b_y2 <- seq(from = sqrt3/2, to = 0, length.out = 11)

b_x4 <- seq(from = 1, to = 0.5, length.out = 11)
b_y4 <- seq(from = 0, to = sqrt3/2, length.out = 11)


# Plot window

    # Continuous color legend
    # Note that it disappears EVERY BLACK LINE!!!!!!
    # So, for the ones you want, you must do col = "black"
    # For more, see here
    # https://stackoverflow.com/questions/8068366/removing-lines-within-filled-contour-legend

    par(fg = NA)


   # Filled contoure plot in base R
    filled.contour(x1, x2, mat,

                  # Number of levels
                  # the greater the more interpolate
                   nlevels = 200,

                  # Colors with base R

                  # Select color function
                   color.palette = colorRampPalette( c( "blue",
                                                        "cyan",
                                                        "yellow",
                                                        "red") ),


                  # Adjust axes to points
                   plot.axes = {
                               ## Manual axes
                               # Axis 1
                                text(b_x1, b_y1,
                                     c("","0.1", "0.2", "0.3", "0.4", "0.5",
                                       "0.6", "0.7", "0.8", "0.9", ""),
                                     adj = c(0.5, 1.5),
                                     col = "black",
                                     cex = 1);


                               # Axis 2
                                text(b_x2, b_y2,
                                     c("","0.1", "0.2", "0.3", "0.4", "0.5",
                                       "0.6", "0.7", "0.8", "0.9", ""),
                                     adj = c(1.25, -0.15),
                                     col = "black",
                                     cex = 1);


                               # Axis 4
                                text(b_x4, b_y4,
                                     c("","0.1", "0.2", "0.3", "0.4", "0.5",
                                       "0.6", "0.7", "0.8", "0.9", ""),
                                     adj = c(-0.25, -0.15),
                                     col = "black",
                                     cex = 1);

                       if ( appear ){
                          nam2 <- colnames(x)
                          if ( !is.null(nam2) )  nam <- nam2
                          proj <- matrix(c(0, 1, 0.5, 0, 0, sqrt3/2), ncol = 2)
                          xa <- x %*% proj
                          points(xa[, 1], xa[, 2], col = "black")
                          };

                          # Show corner titles
                          text(b[1, 1], b[1, 2] + 0.07, nam[3], cex = 1, col = "black", font = 2);
                          text(b[2:3, 1], b[2:3, 2] - 0.07, nam[1:2], cex = 1, col = "black", font = 2);

                               # Draw triangle in two dimensions
                                points(b[, 1], b[, 2],
                                       type = "l",
                                       lwd = 4.5,
                                       col = "black");

                               # Add contour lines
                            if ( cont.line ) {
                                 contour(x1, x2, mat,
                                         pt = "s",
                                        # Color of contour lines
                                        # Otherwise par(fg = NA) will
                                        # disappear them...

                                         col="black",


                                        # Number of levels
                                        nlevels = 7,

                                        # Size of contour numbers
                                         labcex = 0.8,

                                        # Width of contour lines
                                         lwd = 1,

                                         add = TRUE) }
                   },

                  # Legend tick lines
                   key.axes = {axis(4, col = "black")},

                  # Axes labs
                   xlab = "",
                   ylab = "",

                  # Plot limits
                   xlim = c(-0.1, 1.1),
                   ylim = c(-0.1, 1.1) )

# Plot window
}