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POUse 2 grouping variables in a 3D lattice plot in R
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copied!<p>I'm trying to produce a 3D cloud plot using the lattice package in R. I'd like colors and symbols to be grouped by two different factors on the plot. I found this example of how to do this using <code>xyplot</code>, but i'm having trouble adapting it for the <code>cloud</code> function (see code for Fig. 9.2):</p> <p><a href="http://lmdvr.r-forge.r-project.org/figures/figures.html?chapter=09;figure=09_02;theme=stdBW;code=right" rel="nofollow">http://lmdvr.r-forge.r-project.org/figures/figures.html?chapter=09;figure=09_02;theme=stdBW;code=right</a></p> <p>In particular, there is a "subscripts" argument in <code>panel.xyplot</code> that is not present in <code>panel.cloud</code>, and i'm not sure how to change that part of my code.</p> <p>Here's a self contained example of what i'm doing using the <code>mtcars</code> data set. The commented out code in the "panel = " part of the <code>cloud</code> call is what I want to fix. I'd like to color the data points by the variable <code>cyl</code>, and use different symbols to denote different clusters (from a kmeans analysis). Any suggestions are much appreciated.</p> <pre><code># data data(mtcars) # kmeans set.seed(321) km <- kmeans(x = mtcars[, c(1, 3:7)], centers = 3, nstart = 1000) mtcars$cluster <- factor(km$cluster) mtcars$cyl <- factor(mtcars$cyl) # pca form <- formula(c("~", paste0(colnames(mtcars[, c(1, 3:7)]), collapse = "+"))) pca <- prcomp(form, data = mtcars[, c(1, 3:7)]) library(lattice) library(RColorBrewer) # set colors and points colr <- brewer.pal(3, "Set1") pchr <- 0:2 # set plot options par.set <- list(axis.line = list(col = "transparent"), clip = list(panel = "off"), superpose.symbol = list(pch = pchr, col = colr)) # cloud plot cloud(x[, "PC3"] ~ x[, "PC1"] * x[, "PC2"], data = pca, zlab = "PC3", xlab = "PC1", ylab = "PC2", cex = 1, groups = mtcars$cluster, type = "p", main = "3 cluster solution", screen = list(z = 20, x = -70, y = 3), par.settings = par.set, scales = list(col = "black"), #panel = function(x, y, z, subscripts, ...) { # pch <- pchr[mtcars$cluster[subscripts]] # col <- colr[mtcars$cyl[subscripts]] # panel.cloud(x, y, z, pch = pch, col = col) }, key = list(points = list(type = "p", pch = pchr, col = "black", cex = 1.2), text = list(paste("Cluster", levels(mtcars$cluster))), points = list(type = "p", pch = 1, col = colr, cex = 1.2), text = list(paste("Cyl", levels(mtcars$cyl))), columns = 1)) </code></pre>

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