Heatmap with continuous rainbow colours

Question

First of all I have to say that I read many threads about heatmap and ggplot2 here in stackoverflow and elsewhere. But my problem isn't solved yet.

I have got the following dataset:

   Var1   Var2 value
1 -197.5 -197.5     0
2 -192.5 -197.5     0
3 -187.5 -197.5     0
4 -182.5 -197.5     0
5 -177.5 -197.5     0
6 -172.5 -197.5     0
.....

The value should be the colour, and a legend on the right side would be nice.

library(ggplot2)
ggheatmap <- ggplot(data = dat.plot, aes(x=Var1, y=Var2, fill=value)) + 
  geom_raster()+
  scale_fill_gradientn(colours=rainbow(100))+
  theme(axis.text.x = element_text(angle = 0))+ 
  coord_fixed()
print(ggheatmap)

The result is:

I would like to have a "normal" rainbow scale from red=high over orange, yellow, green, light blue, dark blue=low without giving fixed discrete colours as one can do it, e.g. with scale_fill_gradient2. I wonder why "rainbow" starts with red=high end ends with some other red...

The other question: How can I add something to "smooth" the heatmap so that one doesn't see the "edges" everywhere?

Answer 1

The problem of interpolating colors with a complex color scale is best illustrated on the "old faithful" data.

If you use your user defined "rainbow" color scale, the interpolation will not be doing so great (even if the result still looks quite good).

Without interpolation

library(ggplot2)
cols <- rev(rainbow(7)[-7])

ggplot(faithfuld, aes(waiting, eruptions)) +
  geom_raster(aes(fill = density), interpolate = FALSE) +
  scale_fill_gradientn(colours = cols)

With interpolation

ggplot(faithfuld, aes(waiting, eruptions)) +
  geom_raster(aes(fill = density), interpolate = TRUE) +
  scale_fill_gradientn(colours = cols)

With interpolation and a less complex palette

ggplot(faithfuld, aes(waiting, eruptions)) +
  geom_raster(aes(fill = density), interpolate = TRUE) +
  scale_fill_gradientn(colours = c("steelblue", "tomato"))

Answer 2

ggheatmap <- ggplot(data = dat.plot, aes(x=Var1, y=Var2, fill=value)) + 
  geom_raster(interpolate=TRUE)+
  scale_fill_gradientn(colors=rev(c("darkred", "red", "orange", "yellow",    "green", "lightgreen", "lightblue", "darkblue")))+
  theme(axis.text.x = element_text(angle = 0))+ 
  coord_fixed()
print(ggheatmap)

Now it looks blurred. But o.k. If you think it can't be done better, I let it as it is. Thank you very much!

Answer 3

Short answer: function rainbow() goes nuts when you pass 100 as you're asking for 100 different colors.

What should you do: pass n to rainbow() for how many colors you want. If you want to go from blue to red then you also have to wrap it with function rev().

library(egg)
library(ggplot2)
library(reshape2)

# Heatmap number of rows/columns
Nvalue <- 1e2
# n for colors passed to function rainbow
nColor <- c(1:10, seq(20, 100, 20))
# dummy data
df <- melt(matrix(rnorm(N^2), N))

plotList <- list()
for(i in seq_along(nColor)) {
    plotList[[i]] <- ggplot(df, aes(Var1, Var2, fill = value)) + 
        geom_raster() +
        scale_fill_gradientn(colours = rev(rainbow(nColor[i]))) +
        labs(title = paste0("rainbow(", nColor[i], ")"),
             x = NULL,
             y = NULL,
             fill = NULL) +
        theme_void()
}

ggarrange(plots = plotList)

Edit:

After OP specified colors he wants then passing hex vector should work:

hex <- c("#FF0000", "#FFA500", "#FFFF00", "#008000", "#9999ff", "#000066")
ggplot(df, aes(Var1, Var2, fill = value)) + 
        geom_raster() +
        scale_fill_gradientn(colours = rev(hex)) +
        labs(x = NULL,
             y = NULL,
             fill = NULL) +
        theme_void()