overlay 2 images with transparency in R

Here's one option, using rasterImage from base R.

First lets get two images. For the first we read in the R logo jpeg. Then add another array layer to hold the alpha channel (jpegs do not have transparency)

img.logo = jpeg::readJPEG(system.file("img", "Rlogo.jpg", package="jpeg"))
img.logo = abind::abind(img.logo, img.logo[,,1]) # add an alpha channel

For the second image, lets make it an array the same dimensions as img.1, but fill it with random colors

img.random = img.logo
img.random[] = runif(prod(dim(img.random))) # this image is random colors

Now lets set the base image to fully opaque, and the R logo to semi-transparent

img.logo[,,4] = 0.5  # set alpha to semi-transparent
img.random[,,4] = 1  # set alpha to 1 (opaque)

Now we have our example images, we can superimpose them using rasterImage.

png('test.png', width = 2, height = 2, units = 'in', res = 150)
  par(mai=c(0,0,0,0))
  plot.new()
  rasterImage(img.random, 0, 0, 1, 1)
  rasterImage(img.logo,   0, 0, 1, 1)
dev.off()