rheatmapcirclizecomplexheatmap

Is there a way to alphabetize groups within a circular visualization in R using circos.heatmap?


I use R and "circlize" package. I'm trying to create a circular heatmap and I want to sort them alphabetically within the groups. However, I couldn't find how to do it. How can I achieve this?

Figure1: Circular Heatmap with Group Names To produce this graph the code is below:

set.seed(123)
mat1 = rbind(cbind(matrix(rnorm(50*5, mean = 1), nr = 50), 
                   matrix(rnorm(50*5, mean = -1), nr = 50)),
             cbind(matrix(rnorm(50*5, mean = -1), nr = 50), 
                   matrix(rnorm(50*5, mean = 1), nr = 50))
)
rownames(mat1) = paste0("R", 1:100)
colnames(mat1) = paste0("C", 1:10)
mat1 = mat1[sample(100, 100), ] # randomly permute rows
split = sample(letters[1:5], 100, replace = TRUE)
split = factor(split, levels = letters[1:5])

library(circlize) # >= 0.4.10
col_fun1 = colorRamp2(c(-2, 0, 2), c("blue", "white", "red"))

circos.heatmap(mat1, split = split, col = col_fun1, rownames.side = "outside",
               rownames.col = 1:nrow(mat1) %% 10 + 1,
               rownames.cex = runif(nrow(mat1), min = 0.3, max = 2),
               rownames.font = 1:nrow(mat1) %% 4 + 1)


circos.clear()

See Figure1, I will have some groups and I want to sort them alphabetically. What I mean is:

Figure2: A part of Circular Heatmap

For example, for group A, I want to sort it alphabetically. I should only consider group A as sorting the group. I will apply that to all of the groups. How do I do it?


Solution

  • You can sort the labels in your dataset and use cluster = FALSE in circos.heatmap(). Here is the example code that you can modify according to your dataset.

    library(circlize)
    library(stringr)
    
    set.seed(123)
    mat1 = rbind(cbind(matrix(rnorm(50*5, mean=1), nr=50),
                       matrix(rnorm(50*5, mean= -1), nr=50)),
                 cbind(matrix(rnorm(50*5, mean= -1), nr=50),
                       matrix(rnorm(50*5, mean=1), nr=50)))
    
    rownames(mat1) = paste0("R",1:100)
    colnames(mat1) = paste0("C", 1:10)
    mat1 = mat1[sample(100, 100), ] # randomly permute rows
    mat1 = mat1[str_sort(rownames(mat1), numeric = TRUE),]  #sorting the labels for heatmap
    split = sample(letters[1:5], 100, replace = TRUE) 
    split = factor(split, levels = letters[1:5])
    
    #the circular heatmap
    circos.clear()
    col_fun1 = colorRamp2(c(-2, 0, 2), c("blue", "white", "red"))
    circos.heatmap(mat1, split = split, col = col_fun1, 
    rownames.side = "outside", cluster=FALSE,
    rownames.col = 1:nrow(mat1) %% 10 + 1,
    rownames.cex = runif(nrow(mat1), min = 0.3, max = 2),
    rownames.font = 1:nrow(mat1) %% 4 + 1)
    

    enter image description here