R/ggregbiplot.R

In gfalbery/ggregplot:

# ggregbiplot ####

ggregbiplot <- 
  function (pcobj, choices = 1:2, scale = 1, pc.biplot = TRUE, 
            obs.scale = 1 - scale, var.scale = scale, groups = NULL, 
            ellipse = FALSE, ellipse.prob = 0.68, labels = NULL, labels.size = 3, 
            alpha = 1, var.axes = TRUE, circle = FALSE, circle.prob = 0.69, 
            varname.size = 3, varname.adjust = 1.5, varname.abbrev = FALSE, 
            ...) 
  {
    require(ggplot2)
    require(plyr)
    require(scales)
    require(grid)
    stopifnot(length(choices) == 2)
    if (inherits(pcobj, "prcomp")) {
      nobs.factor <- sqrt(nrow(pcobj$x) - 1)
      d <- pcobj$sdev
      u <- sweep(pcobj$x, 2, 1/(d * nobs.factor), FUN = "*")
      v <- pcobj$rotation
    }
    else if (inherits(pcobj, "princomp")) {
      nobs.factor <- sqrt(pcobj$n.obs)
      d <- pcobj$sdev
      u <- sweep(pcobj$scores, 2, 1/(d * nobs.factor), FUN = "*")
      v <- pcobj$loadings
    }
    else if (inherits(pcobj, "PCA")) {
      nobs.factor <- sqrt(nrow(pcobj$call$X))
      d <- unlist(sqrt(pcobj$eig)[1])
      u <- sweep(pcobj$ind$coord, 2, 1/(d * nobs.factor), FUN = "*")
      v <- sweep(pcobj$var$coord, 2, sqrt(pcobj$eig[1:ncol(pcobj$var$coord), 
                                                    1]), FUN = "/")
    }
    else if (inherits(pcobj, "lda")) {
      nobs.factor <- sqrt(pcobj$N)
      d <- pcobj$svd
      u <- predict(pcobj)$x/nobs.factor
      v <- pcobj$scaling
      d.total <- sum(d^2)
    }
    else {
      stop("Expected a object of class prcomp, princomp, PCA, or lda")
    }
    choices <- pmin(choices, ncol(u))
    df.u <- as.data.frame(sweep(u[, choices], 2, d[choices]^obs.scale, 
                                FUN = "*"))
    v <- sweep(v, 2, d^var.scale, FUN = "*")
    df.v <- as.data.frame(v[, choices])
    names(df.u) <- c("xvar", "yvar")
    names(df.v) <- names(df.u)
    if (pc.biplot) {
      df.u <- df.u * nobs.factor
    }
    r <- sqrt(qchisq(circle.prob, df = 2)) * prod(colMeans(df.u^2))^(1/4)
    v.scale <- rowSums(v^2)
    df.v <- r * df.v/sqrt(max(v.scale))
    if (obs.scale == 0) {
      u.axis.labs <- paste("standardized PC", choices, sep = "")
    }
    else {
      u.axis.labs <- paste("PC", choices, sep = "")
    }
    u.axis.labs <- paste(u.axis.labs, sprintf("(%0.1f%% explained var.)", 
                                              100 * pcobj$sdev[choices]^2/sum(pcobj$sdev^2)))
    if (!is.null(labels)) {
      df.u$labels <- labels
    }
    if (!is.null(groups)) {
      df.u$groups <- groups
    }
    if (varname.abbrev) {
      df.v$varname <- abbreviate(rownames(v))
    }
    else {
      df.v$varname <- rownames(v)
    }
    df.v$angle <- with(df.v, (180/pi) * atan(yvar/xvar))
    df.v$hjust = with(df.v, (1 - varname.adjust * sign(xvar))/2)
    g <- ggplot(data = df.u, aes(x = xvar, y = yvar)) + xlab(u.axis.labs[1]) + 
      ylab(u.axis.labs[2]) + coord_equal()
    if (var.axes) {
      if (circle) {
        theta <- c(seq(-pi, pi, length = 50), seq(pi, -pi, 
                                                  length = 50))
        circle <- data.frame(xvar = r * cos(theta), yvar = r * 
                               sin(theta))
        g <- g + geom_path(data = circle, color = muted("white"), 
                           size = 1/2, alpha = 1/3)
      }
      g <- g + geom_segment(data = df.v, aes(x = 0, y = 0, 
                                             xend = xvar, yend = yvar), arrow = arrow(length = unit(1/2, 
                                                                                                    "picas")), color = muted("red"))
    }
    if (!is.null(df.u$labels)) {
      if (!is.null(df.u$groups)) {
        g <- g + geom_text(aes(label = labels, color = groups), 
                           size = labels.size)
      }
      else {
        g <- g + geom_text(aes(label = labels), size = labels.size)
      }
    }
    else {
      if (!is.null(df.u$groups)) {
        g <- g + geom_point(aes(color = groups), alpha = alpha)
      }
      else {
        g <- g + geom_point(alpha = alpha)
      }
    }
    if (!is.null(df.u$groups) && ellipse) {
      theta <- c(seq(-pi, pi, length = 50), seq(pi, -pi, length = 50))
      circle <- cbind(cos(theta), sin(theta))
      ell <- ddply(df.u, "groups", function(x) {
        if (nrow(x) <= 2) {
          return(NULL)
        }
        sigma <- var(cbind(x$xvar, x$yvar))
        mu <- c(mean(x$xvar), mean(x$yvar))
        ed <- sqrt(qchisq(ellipse.prob, df = 2))
        data.frame(sweep(circle %*% chol(sigma) * ed, 2, 
                         mu, FUN = "+"), groups = x$groups[1])
      })
      names(ell)[1:2] <- c("xvar", "yvar")
      g <- g + geom_path(data = ell, aes(color = groups, group = groups))
    }
    if (var.axes) {
      g <- g + geom_text(data = df.v, aes(label = varname, 
                                          x = xvar, y = yvar, angle = angle, hjust = hjust), 
                         color = "darkred", size = varname.size)
    }
    return(g)
  }