R with diverging color palette

Question

I am trying to create a simple heat map in R using a diverging color palette. I want to use a gradient, so that all numbers below the threshold N are indicated by a color (for example, purple), and all numbers above the threshold are indicated by another color (for example, orange). The farther from the threshold, the darker the color should be.

Here is an example dataset:

Division,COL1,COL2,COL3,COL4,COL5,COL6,COL7 Division 1,31.9221884012222,75.8181694429368,97.0480443444103,96.295954938978,70.5677134916186,63.0451830103993,93.0396212730557 Division 2,85.7012346852571,29.0621076244861,16.9130333233625,94.6443660184741,19.9103083927184,61.9562198873609,72.3791105207056 Division 3,47.1665125340223,99.4153356179595,8.51091076619923,79.1276383213699,41.915355855599,7.45079894550145,24.6946100145578 Division 4,66.0743870772421,24.6163331903517,78.694460215047,42.04714265652,50.2694897353649,73.0409651994705,87.3745442833751 Division 5,29.6664374880493,35.4036891367286,19.2967326845974,5.48460693098605,32.4517334811389,15.5926876701415,76.0523204226047 Division 6,95.4969164915383,8.63230894319713,61.7535551078618,24.5590241160244,25.5453423131257,56.397921172902,44.4693325087428 Division 7,87.5015622004867,28.7770316936076,56.5095080062747,34.6680747810751,28.1923673115671,65.0204187724739,13.795713102445 Division 8,70.1077231671661,72.4712177179754,38.4903231170028,36.1821102909744,97.0875509083271,17.184783378616,78.2292529474944 Division 9,47.3570406902581,90.2257485780865,65.6037972308695,77.0234781783074,25.6294377148151,84.900529962033,82.5080851092935 Division 10,58.0811711959541,0.493217632174492,58.5604055318981,53.5780876874924,9.12552657537162,20.313960686326,78.1371118500829 Division 11,34.6708688884974,76.711881859228,22.6064443588257,22.1724311355501,5.48891355283558,79.1159523651004,56.8405059166253 Division 12,33.6812808644027,44.1363711375743,70.6362190190703,3.78900407813489,16.6075889021158,9.12654218263924,39.9711143691093 

Here is a simple snippet for creating a heat map from the above data.

 data <- read.csv("dataset.csv", sep=",") row.names(data) <- data$Division data <- data[,2:7] data_matrix <- data.matrix(data) heatmap(data_matrix, Rowv=NA, Colv=NA, col = heat.colors(256), scale="column", margins=c(5,10)) 

How can I modify the above code to create:

• color gradient (orange) for all numbers ABOVE 50 (darker the farther from 50)
• color gradient (purple) for all numbers BELOW 50 (darker the farther from 50)
• It's nice to have (but not necessarily) write a numerical value in a grid cell
• It's nice to have (but not necessarily) use a different color for the grid cell, which is EXACTLY a threshold number (in this case 50)

[[Edit]]

I just saw this question on SO , which seems to be very similar. The answer uses ggplot (which I don't have), and so far I have not been able to adapt the ggplot solution to my slightly more complex data.

Answer 1

That should make you most of the way. (Note that you need to set scale="none" if you want the displayed colors to match the actual (rather than scaled) cell values).

 ncol <- 100 ## Make a vector with n colors cols <- RColorBrewer:::brewer.pal(11,"PuOr") # OR c("purple","white","orange") rampcols <- colorRampPalette(colors = cols, space="Lab")(ncol) rampcols[(n/2) + 1] <- rgb(t(col2rgb("green")), maxColorValue=256) ## Make a vector with n+1 breaks rampbreaks <- seq(0, 100, length.out = ncol+1) ## Try it out heatmap(data_matrix, Rowv = NA, Colv = NA, scale="none", col = rampcols, breaks = rampbreaks) 

EDIT

For more precise control over the placement of the threshold, I would suggest creating two separate palettes: one for values ​​less than the threshold, and the other for values ​​above the threshold - and then “stitch” them together. Try something like this, playing with different values ​​for Min , Max , Thresh , etc:

 nHalf <- 50 Min <- 0 Max <- 100 Thresh <- 50 ## Make vector of colors for values below threshold rc1 <- colorRampPalette(colors = c("purple", "white"), space="Lab")(nHalf) ## Make vector of colors for values above threshold rc2 <- colorRampPalette(colors = c("white", "orange"), space="Lab")(nHalf) rampcols <- c(rc1, rc2) ## In your example, this line sets the color for values between 49 and 51. rampcols[c(nHalf, nHalf+1)] <- rgb(t(col2rgb("green")), maxColorValue=256) rb1 <- seq(Min, Thresh, length.out=nHalf+1) rb2 <- seq(Thresh, Max, length.out=nHalf+1)[-1] rampbreaks <- c(rb1, rb2) heatmap(data_matrix, Rowv = NA, Colv = NA, scale="none", col = rampcols, breaks = rampbreaks) 

Answer 2

I found this topic very useful and also pulled some ideas from here , but for my purposes I needed to generalize some things and want to use the RColorBrewer package. While I was working on it, Dr. Brewer (from the celebrity Color Brewer) stopped in my office and told me that I need to interpolate as part of small color gaps, and not just select the end points. I thought others might find this useful, so I post my function here for posterity.

The function accepts your data vector, the name of the diverging colorBrewer palette, and the center point for your color scheme (default is 0). It displays a list containing 2 objects: a classIntervals object and a color vector: the function is configured to interpolate only 100 colors, but this can be changed with some caution.

 diverge.color <- function(data,pal_choice="RdGy",centeredOn=0){ nHalf=50 Min <- min(data,na.rm=TRUE) Max <- max(data,na.rm=TRUE) Thresh <- centeredOn pal<-brewer.pal(n=11,pal_choice) rc1<-colorRampPalette(colors=c(pal[1],pal[2]),space="Lab")(10) for(i in 2:10){ tmp<-colorRampPalette(colors=c(pal[i],pal[i+1]),space="Lab")(10) rc1<-c(rc1,tmp) } rb1 <- seq(Min, Thresh, length.out=nHalf+1) rb2 <- seq(Thresh, Max, length.out=nHalf+1)[-1] rampbreaks <- c(rb1, rb2) cuts <- classIntervals(data, style="fixed",fixedBreaks=rampbreaks) return(list(cuts,rc1)) } 

In my work, I use this scheme to build a raster layer (rs) using spplot as follows:

 brks<-diverge.color(values(rs)) spplot(rs,col.regions=brks[[2]],at=brks[[1]]$brks,colorkey=TRUE))