Question

I have the following data created on the fly:

 > df <- data.frame( cbind(rnorm(200),rnorm(200, mean=.8),rnorm(200, mean=.9),rnorm(200, mean=1),rnorm(200, mean=.2),rnorm(200, mean=.3)),rnorm(200, mean=4),rnorm(200, mean=.5))
 > colnames(df) <- c("w.cancer","w.normal","x.cancer","x.normal","y.cancer","y.normal","z.cancer","z.normal")
 > df_log<-log2(df) # ignore the warning with NA
 > head(df_log)

What I want to do is to create multiple plots in one panel like the sketch below using ‘facet’.
How can I go about it?

Answer 1

You’ll have to prepare your data first. I’ve illustrated this on your data.frame df as it is a proper normal distribution.

require(ggplot2)
require(reshape2)
df$id <- 1:nrow(df)

df.m <- melt(df, "id")
df.m$grp1 <- factor(gsub("\\..*$", "", df.m$variable))
df.m$grp2 <- factor(gsub(".*\\.", "", df.m$variable))

p <- ggplot(data = df.m, aes(x=value)) + geom_density(aes(fill=grp2), alpha = 0.4)
p <- p + facet_wrap( ~ grp1)
p + scale_fill_brewer(palette = "Set1")

Doing the same by replacing df with df_log you’d get something like this:

require(ggplot2)
require(reshape2)
df_log$id <- 1:nrow(df_log)

df.m <- melt(df_log, "id")
df.m$grp1 <- factor(gsub("\\..*$", "", df.m$variable))
df.m$grp2 <- factor(gsub(".*\\.", "", df.m$variable))

p <- ggplot(data = df.m, aes(x=value)) + geom_density(aes(fill=grp2), alpha = 0.5)
p <- p + facet_wrap( ~ grp1)
p