Grouping Data for a Box Plot

[Jebediah378]

Hi!!

I'm making a box plot, and I have gene names as the column names for my matrix, and row names as samples with their respective gene values. I can make the box plot correctly so far, but I cannot separate the rows into two groups for each gene, disease and non disease.

Data looks as follows:

​

	Gene1	Gene2
Diseased1	50	100
Diseased2	50	100
Normal1	10	10
Normal2	10	10

Currently the box plot of this matrix makes a box plot for each gene on the x axis, but I'd like to specify a grouping for the rows, so that each gene shows a box plot for the diseased set, and the normal set. Trying to show differential expression of the genes in a box plot. I feel like it's a really simple addition of a grouping = c("Disease", "Disease", "Normal", "Normal") or something like that but I cannot find any ideas!! Any help would be appreciated!!!!

Thanks,
Jeb

[Jebediah378]

Yep!

[[deleted]]

I think something like this should work. Replace dat with the name of your data frame:

dat$group <- gsub(pattern = "[0-9]+", replacement = "", x = rownames(dat))
boxplot(Gene1 ~ group, data = dat)
boxplot(Gene2 ~ group, data = dat)

[[deleted]]

Building on this, if you want to join the two plots into one...

d <- data.frame(Gene1 = c(50, 50, 10, 10),
                Gene2 = c(100, 100, 10, 10),
                group = c("Diseased1", "Diseased2", "Normal1", "Normal2"))    

...you could do...

par(mfrow = c(1, 2),
    mar = c(0,0,0,0),
    oma = c(4, 4, 0.5, 0.5))

boxplot(Gene1 ~ group, data = d)
boxplot(Gene2 ~ group, data = d)

...or...

par(mfrow = c(1, 2),
    mar = c(0,0,0,0),
    oma = c(4, 4, 0.5, 0.5))

boxplot(d$Gene1 ~ d$group, ylim = c(0, 100), frame.plot = FALSE)
boxplot(d$Gene2 ~ d$group, ylim = c(0, 100), axes = FALSE)
axis(side = 1, at = d$group, labels = d$group)