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POSweep warnings when using ggbiplot to plot FactoMineR's PCA object
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I'm trying to adapt <a href="https://github.com/vqv/ggbiplot" rel="nofollow noreferrer">ggbiplot</a> to work with the <code>PCA</code> data object produced by the <code>FactoMineR</code> package but I'm getting warnings I don't understand. Here's what I've done so far, I've added the bit starting at <code>else if(inherits(pcobj, 'PCA'))</code> and ending at the next <code>}</code> using details I've found on the <code>FactoMineR</code> email list. I haven't changed anything elsewhere in the code, which is reproduced here entirely: <pre><code> ggbiplot <- 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, ...) { library(ggplot2) library(plyr) library(scales) library(grid) stopifnot(length(choices) == 2) # Recover the SVD 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 { stop('Expected a object of class prcomp, princomp or PCA') } # Scores df.u <- as.data.frame(sweep(u[,choices], 2, d[choices]^obs.scale, FUN='*')) # Directions 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 } # Scale the radius of the correlation circle so that it corresponds to # a data ellipse for the standardized PC scores r <- sqrt(qchisq(circle.prob, df = 2)) * prod(colMeans(df.u^2))^(1/4) # Scale directions v.scale <- rowSums(v^2) df.v <- r * df.v / sqrt(max(v.scale)) # Change the labels for the axes if(obs.scale == 0) { u.axis.labs <- paste('standardized PC', choices, sep='') } else { u.axis.labs <- paste('PC', choices, sep='') } # Append the proportion of explained variance to the axis labels u.axis.labs <- paste(u.axis.labs, sprintf('(%0.1f%% explained var.)', 100 * pcobj$sdev[choices]^2/sum(pcobj$sdev^2))) # Score Labels if(!is.null(labels)) { df.u$labels <- labels } # Grouping variable if(!is.null(groups)) { df.u$groups <- groups } # Variable Names if(varname.abbrev) { df.v$varname <- abbreviate(rownames(v)) } else { df.v$varname <- rownames(v) } # Variables for text label placement df.v$angle <- with(df.v, (180/pi) * atan(yvar / xvar)) df.v$hjust = with(df.v, (1 - varname.adjust * sign(xvar)) / 2) # Base plot 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) { # Draw circle 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) } # Draw directions 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')) } # Draw either labels or points 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$groups)) { g <- g + geom_point(aes(color = groups), alpha = alpha) } else { g <- g + geom_point(alpha = alpha) } } # Overlay a concentration ellipse if there are groups if(!is.null(df.u$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) } else if(nrow(x) == 2) { sigma <- var(cbind(x$xvar, x$yvar)) } else { sigma <- diag(c(var(x$xvar), var(x$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$groups[1]) }) names(ell)[1:2] <- c('xvar', 'yvar') g <- g + geom_path(data = ell, aes(color = groups, group = groups)) } # Label the variable axes if(var.axes) { g <- g + geom_text(data = df.v, aes(label = varname, x = xvar, y = yvar, angle = angle, hjust = hjust), color = 'darkred', size = varname.size) } # Change the name of the legend for groups # if(!is.null(groups)) { # g <- g + scale_color_brewer(name = deparse(substitute(groups)), # palette = 'Dark2') # } return(g) } </code></pre> It produces a plot, like so: <pre><code>library(FactoMineR) data(decathlon) res.pca <- PCA(decathlon, quanti.sup = 11:12, quali.sup=13, graph=FALSE) ggbiplot(res.pca) </code></pre> <img src="https://i.stack.imgur.com/kfO3R.png" alt="enter image description here"> But it also produces these warnings, which I don't understand (@baptiste's suggestion removed a bunch of other warnings): <pre><code> Warning messages: 1: In sweep(pcobj$ind$coord, 2, 1/(d * nobs.factor), FUN = "*") : STATS is longer than the extent of 'dim(x)[MARGIN]' 2: In sweep(v, 2, d^var.scale, FUN = "*") : STATS is longer than the extent of 'dim(x)[MARGIN]' </code></pre> How do I fix the <code>ggbiplot</code> code so it doesn't produce these warnings when plotting a <code>PCA</code> object? I'm worried they might be causing the output to be not what I'm expecting.
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<r><plot><ggplot2><pca><ggbiplot>
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Sweep warnings when using ggbiplot to plot FactoMineR's PCA object
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1. COfor one thing, you probably want `if('prcomp' %in% class(pcobj))` or better yet, `if(inherits(pcobj, 'prcomp'))`; that should help with 3 to 5.
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 POSweep warnings when using ggbiplot to plot FactoMineR's PCA object
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2. COGreat suggestion, thanks. Those warnings have disappeared now that I've added your lines. I've updated my question accordingly.
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 POSweep warnings when using ggbiplot to plot FactoMineR's PCA object
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