Rescaling colors palette in r

Question

In R i have a cloud of data around zero ,and some data around 1, i want to "rescale" my heat colors to distinguish lower numbers.This has to be done in a rainbow way, i don't want "discrete colors".I tried with breaks in image.plot but it doesn't work.

  image.plot(X,Y,as.matrix(mymatrix),col=heat.colors(800),asp=1,scale="none")

I tried :

lowerbreak=seq(min(values),quantile2,len=80)
  highbreak=seq(quantile2+0.0000000001,max(values),len=20)
  break=c(lowerbreak,highbreak)
  ii <- cut(values, breaks = break, 
            include.lowest = TRUE)

  colors <- colorRampPalette(c("lightblue", "blue"))(99)[ii]

I tried but i'm not able to understand how can i do to distinguish low value — lgndrzzz, Oct 13 '17 at 10:30

score 2 · Answer 1 · answered Oct 13 '17 at 11:01

2

When using colorRampPalette, you can set the bias argument to emphasise low (or high) values.

Something like colorRampPalette(heat.colors(100),bias=3) will result focus the 'ramp' on the lower, helping them to be more visually distinguishable.

answered Oct 13 '17 at 11:01

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I have to put a too much high bias that make the color ramp all yellow without shadows – lgndrzzz Oct 13 '17 at 13:05

Keegan Smith · Accepted Answer · 2018-09-01T17:13:47.787

Here's an approach using the "squash" library. With makecmap(), you specify your colour values and breaks, and you can also specify that it should be log stretched using the base parameter. It's a bit complex, but gives you granular control. I use it to colorize skewed data, where I need more definition in the "low end".

To achieve the rainbow palette, I used the built-in "jet" colour function, but you can use any colour set - I give an example for creating a greyscale ramp with "colorRampPalette".

Whatever ramp you use, it will take some playing with the base value to optimize for your data.

install.packages("squash")
library("squash")

#choose your colour thresholds - outliers will be RED
minval=0   #lowest value to get a colour
maxval=2.0 #highest value to get a colour
n.cols=100 #how many colours do you want in your palette?
col.int=1/n.cols

#create your palette
colramp=makecmap(x=seq(minval,maxval,col.int),
                 n=n.cols,
                 breaks=prettyLog,
                 symm=F,
                 base=10,#to give ramp a log(base) stretch
                 colFn=jet,
                 col.na="red",
                 right=F,
                 include.lowest=T)

# If you don't like the colFn options in "makecmap", define your own!
#   Here's an example in greyscale; pass this to "colFn" above
user.colfn=colorRampPalette(c("black","white"))

Example for using colramp in a plot (assuming you've already created colramp as above somewhere in your program):

varx=1:100
vary=1:100
plot(x,y,col=colramp$colors) #colors is the 2nd vector in the colramp list

To select specific colours, subset from the list via, e.g., colors[1:20] (if you try this with the example above, the first colors will repeat 5 times - not really useful but you get the logic and can play around).

In my case, I had a grid of values that I wanted to turn into a coloured raster image (i.e. colour mapping some continuous data). Here's example code for that, using a made up matrix:

#create a "dummy matrix"
matx=matrix(data=c(rep(2,50),rep(0,500),rep(0.5,500),rep(1,500),rep(1.5,500)),nrow=50,ncol=41,byrow=F)

#transpose the matrix
#  the output of "savemat" is rotated 90 degrees to the left
#  so savemat(maty) will be a colorized version of (matx)
maty=t(matx)

#savemat creates an image using colramp
savemat(x=maty,
    filename="/Users/KeeganSmith/Desktop/matx.png",
    map=colramp,
    outlier="red",
    dev="png",
    do.dev.off=T)

I've edited my answer to include example code for a simple plot and simple matrix -> raster image creation. — Keegan Smith, Sep 01 '18 at 17:14

Rescaling colors palette in r

2 Answers2