v <- stack(mymatrix[-1])
v$Treatment <- mymatrix$Treatment
boxplot(values~Treatment+ind, v)
The first part will give us a data.frame
like this:
values ind
1 13 c1
2 93 c1
...
11 82 c1
12 33 c5
...
22 9 c5
23 96 c3
...
55 25 c12
Then we append the Treatment
column, and just plot as usual.
update: using the reshape
package as suggested by Drew.
v <- melt(mymatrix, id.vars="Treatment")
boxplot(value~Treatment+variable, v)