R Heatmap Notes

heatmap_r

# Instructions
# `d` is the example datastructure
# `n` in kde2d is the granularity of the heatmap. It's how many pixels appears on the vertical and horizontal axes (total pixels is n^2)
# `n` in colours / rainbow controls the colors of the heatmap rainbow. 
# `cuts` in levelplot also controls the smoothness of the color bleeding between pixels. 
# - I don't think `cuts` can be set to more than the integer in `col.regions=rgb.palette(150)`. 

#  package
require(lattice)
require(MASS)


# original data
d <- structure(list(
  X = c(-60L, 60L, 7L, -22L, 59L, 29L, -58L, 60L, 
                          7L, -21L, 61L, 29L, -57L, -22L, 59L, 29L, -56L, 61L, 8L, -20L, 
                          62L, 30L), 
  Y = c(-18L, -62L, 14L, -60L, 58L, 22L, -18L, -61L, 
                                           14L, -59L, 59L, 22L, -18L, -59L, 60L, 24L, -17L, -60L, 16L, -58L, 
                                           60L, 23L)), 
  .Names = c("X", "Y"), class = "data.frame", row.names = c(NA, -22L))



# use mass' kde2d to convert x,y to matrix
dens <- kde2d(d$X, d$Y, h=75, n=50)  #overrode default bandwidth


# insert notes on smoothing matrix.....


# Colors
n=10
colours = rainbow(n, s = 1, v = 1, start = 0, end = max(1, n - 1)/n, alpha = 1)

rgb.palette <- colorRampPalette(colours, space = "Lab")


# The use of levelplot is really easy then:
levelplot(dens$z, col.regions=rgb.palette(150), scales=list(x=list(cex=.3), y=list(cex=.3)), 
          main="Main Title", 
          xlab="Samples", 
          ylab="Samples" ,
          cuts = 150)