Boxplot of 2 groups in R with graphics::boxplot

Question

I have 2 groups of data (top and bottom) that I have been able to make boxplots for separately, but cannot get them to show in the same graph. I want them side by side for comparison for each gene tested (12 total). So, I would like to have the x-axis labeled with the gene tested, and the y-axis with the ddCt values, with 2 boxplots (1 for the top, 1 for the bottom) for each gene. I have the code for each one separately that works below:

# boxplot of first group
boxplot(Top25[-1], main = "Top Performers Gene Expression Relative to 16S", ylab = "ddCt Values", xlab = "Biofilm Gene", cex.axis = 0.75)

# boxplot of second group 
boxplot(Bottom25 [-1], main = "Bottom Performers Biofilm Gene Expression Relative to 16S", ylab = "ddCt Values", xlab = "Biofilm Gene", cex.axis = 0.75)

Any suggestions for what I may try? I've tried to "melt" them together following another ggplot2 question and got an error saying "object melt was not found". Thanks for any help!

Answer 1

Here is an example. The main idea is to use add = TRUE to add boxplot to an existing plot and specify the horizontal position of boxplot with at

#DATA
set.seed(42)
top = rnorm(40)
bottom = rnorm(40)

#Create Empty Plot
plot(1, 1, type = "n", xlim = c(0, 3), ylim = range(c(top, bottom)),
     ann = FALSE, xaxt = "n")

#Add boxplots to existing plot
boxplot(x = top, at = 1, add = TRUE)
boxplot(x = bottom, at = 2, add = TRUE)
axis(1, at = c(1, 2), labels = c("top", "bottom"))

Answer 2

You can do this:

Top25 <- data.frame(gene=1:40, exp=rnorm(40, 2))
Bottom25 <- data.frame(gene=41:80, exp=rnorm(40, -2))

boxplot(list(Top25[, -1], Bottom25[, -1]), names=c("Top25", "Bottom25"))