I am working with an R library ‘aweSOM.’ The library has a plot ‘aweSOMplot’ with palettes restricted to RcolorBrewer.

Of course, Viridis + Viridis mako are a subset of the RcolorBrewer library. However, when I try to select a subset or direction for the viridis palettes in the aweSOMplot, it doesn’t seem to work.

I wondered if someone could help me change the source code below (or the script code) such that the mako palette is available, and from the mako palette I can choose a subset of the palette for the ‘palsc’ argument.

Any help would be appreciated.

#############
#AWESOM PLOT
##############

install.packages("aweSOM")
install.packages("kohonen")
install.packages("RColorBrewer")

library(aweSOM)
library(kohonen)
library(RColorBrewer)

#DATA 

X1 <- rep(1:3, times = 100)
X1 <- sample(X1)
X2 <- rep(1:3, times = 100)
X2 <- sample(X2)
X3 <- rep(1:3, times = 100)
X3 <- sample(X3)
X4 <- rep(1:3, times = 100)
X4 <- sample(X4)
X5 <- rep(1:3, times = 100)
X5 <- sample(X5)

Dat <- data.frame(X1, X2, X3, X4, X5)
Dat <- data.frame(lapply(Dat, function(x) as.numeric(as.character(x))))
Dat <- as.matrix(Dat)

#SET SEED

set.seed(145)

#SOM INITIALISATION

init <- somInit(Dat, 3, 3)

#SOM OBJECT

SOM <- kohonen::som(Dat, grid = kohonen::somgrid(3, 3, "hexagonal"), 
                           rlen = 100, alpha = c(0.05, 0.01),
                           dist.fcts = "manhattan", init = init, keep.data = TRUE)

#CLUSTERING ON THE SOM

threeclusters3x3 <- cluster::pam(SOM$codes[[1]], 3)
clus3x3 <- threeclusters3x3$clustering

#PLOTTING THE SOM

plot < - aweSOMplot(som = SOM, type = "Barplot", data = Dat, 
                    variables = c("X1", "X2", "X3", "X4", "X4"),
                    superclass = clus3x3,
                    showAxes = FALSE,
                    values = "median", 
                    palsc = "Blues",
                    palvar = "Greys")

plot

######################
## SOURCE CODE
#######################

getPalette <- function(pal, n, reverse= F) {
  if(pal == "grey") {
    res <- grey(1:n / n)
  } else if(pal == "rainbow") { 
    res <- substr(rainbow(n), 1, 7) 
  } else if(pal == "heat") { 
    res <- substr(heat.colors(n), 1, 7) 
  } else if(pal == "terrain") { 
    res <- substr(terrain.colors(n), 1, 7) 
  } else if(pal == "topo") { 
    res <- substr(topo.colors(n), 1, 7) 
  } else if(pal == "cm") { 
    res <- substr(cm.colors(n), 1, 7) 
  } else if (pal == "viridis") {
    if (n == 1) {
      res <- substr(viridis::viridis(3), 1, 7)[1]
    } else if (n == 2) {
      res <- substr(viridis::viridis(3), 1, 7)[c(1,3)]
    } else 
      res <- substr(viridis::viridis(n), 1, 7)
  } else {
    if (n == 1) {
      res <- RColorBrewer::brewer.pal(3, pal)[1]
    } else if (n == 2) {
      res <- RColorBrewer::brewer.pal(3, pal)[c(1,3)]
    } else 
      res <- RColorBrewer::brewer.pal(n, pal)
  }
  if (length(res) == 1) 
    res <- list(res)
  if (reverse) 
    res <- rev(res)
  res
}