I have recently used the following script in order to perform a MCA analysis and visualize the plot (I found it on http://gastonsanchez.com/blog/how-to/2012/10/13/MCA-in-R.html).
The data are from the Data frame "Tea" contained in the R package "FactoMineR".
# load data tea
data(tea)
# select these columns
newtea = tea[, c("Tea", "How", "how", "sugar", "where", "always")]
# number of categories per variable
cats = apply(newtea, 2, function(x) nlevels(as.factor(x)))
# apply MCA
mca1 = MCA(newtea, graph = FALSE)
# data frame with variable coordinates
mca1_vars_df = data.frame(mca1$var$coord, Variable = rep(names(cats), cats))
# data frame with observation coordinates
mca1_obs_df = data.frame(mca1$ind$coord)
# plot of variable categories
ggplot(data=mca1_vars_df,
aes(x = Dim.1, y = Dim.2, label = rownames(mca1_vars_df))) +
geom_hline(yintercept = 0, colour = "gray70") +
geom_vline(xintercept = 0, colour = "gray70") +
geom_text(aes(colour=Variable)) +
ggtitle("MCA plot of variables using R package FactoMineR")
It runs perfectly, but I would like to know how to introduce qualitative supplementary variables in the analysis. Since I'm not familiar with ggplot2 at all, I'm a bit lost here.
For instance, if I wanted "Tea" to be the supplementary variable, how should I modify the script?
#apply MCA
mca1 = MCA(newtea, graph = FALSE,quali.sup=1)
But how can I preserve this information in the ggplot script?