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rplotlattice

Color gradient for elevation data in a XYZ plot with R and Lattice

I have a bunch of XYZ data where X and Y are coordinates and Z is supposed to be the elevation (LiDAR points). I am trying to plot this point cloud with a gradient based on the Z value.

Here is what I have so far: 

# Read the CSV file with the LiDAR point cloud (which was conveniently converted to CSV)
myData <- read.csv("./52I212_plot10.las.csv")
# We don't need all attributes, let's keep only X, Y and Z.
myData <- subset(myData, select=c(X,Y,Z))
# We want a normalized version of Z (between 0 and 1)
myData$normalZ <- (myData$Z-min(myData$Z))/(max(myData$Z)-min(myData$Z))
str(myData)

With this I try to create the plot with

library(lattice)
ramp <- colorRampPalette(c("lightblue", "red"))
cloud(myData$Z ~ myData$X + myData$Y, xlab="X", ylab="Y", zlab="Z",pch=20,
  col.point=ramp(10)[myData$normalZ*10])

I expected Z values to have one of ten possible colors between lightblue and red. XYZ plot, different colors

When I change the plot command to

cloud(myData$Z ~ myData$X + myData$Y, xlab="X", ylab="Y", zlab="Z",pch=20,
  col.point=gray(myData$normalZ))

I get something that is much closer to what I need:

Much better!

I suspect I am doing something wrong on the color ramp, but cannot figure out what.

thanks in advance

Rafael

EDIT

This question: How to match vector values with colours from a colour ramp in R? helped me a lot, but I still don't understand what I did wrong. This code works:

myData$normalZ <- (myData$Z-min(myData$Z))/(max(myData$Z)-min(myData$Z))
ramp <- colorRamp(c("lightblue", "red"))
cols <- ramp(myData$normalZ)
cloud(myData$Z ~ myData$X + myData$Y, xlab="X", ylab="Y", zlab="Z",pch=20,
      col.point=rgb(cols,maxColorValue = 256))

Aha!

Please point what could be changed on the original code to make it work -- I cannot figure out why in the first figure colors appear to be randomish.

thanks Rafael

Solution

  • Can't confirm without data, but I think 0's are throwing you off. Your normalZ is between 0 and 1, so 10 * normalZ is between 0 and 10. You're passing these non-integers to [ and they get rounded down. (I had to look this up, but from ?"[": "Numeric values [of i] are coerced to integer as by as.integer (and hence truncated towards zero)".

    Giving 0 (or anything less than 1) as a subset index messes with your color vector's length and hence how things match up:

    ramp(10)[c(0, 0.4, 0.8, 1.2, 1.6)]
# [1] "#ACD8E5" "#ACD8E5"

    and then the too-short vector gets recycled. So, your code will probably work with 

    col.point = ramp(10)[ceiling(myData$normalZ * 10)]