Subscripts in plots in R

expression is your friend:

plot(1,1, main=expression('title'^2))  #superscript
plot(1,1, main=expression('title'[2])) #subscript

If you are looking to have multiple subscripts in one text then use the star(*) to separate the sections:

plot(1:10, xlab=expression('hi'[5]*'there'[6]^8*'you'[2]))

See ?expression

plot(1:10,main=expression("This is a subscript "[2]))