# Generate a raster to play with
library(raster)
library(RStoolbox)
mat = matrix(c(1,2,4,4),nrow=2,ncol=2)
ras=raster(mat)

# Use ggplot2::fortify() to turn it into a data.frame
ras.fort = ggplot2::fortify(ras)

# Select the raster values you're interested in (here, for example, 4)
mylocs = ras.fort[ras.fort$layer==4,]
# `x` and `y` columns are your coordinates

> r = raster(matrix(runif(50*50),50,50))
> coords = coordinates(r)[r[]>0.9,]

> plot(r)
> points(coords)