rheatmapcirclize

Circular heatmap with R "circlize": Plot area and row labels

I'm trying to plot a single circular clustered heatmap with dendrogram with R "circlize" package. The two column expression data is available from this pastebin link

I'm using the following code for plotting, mostly lifted from the circlize manual:

dataURL <- "https://pastebin.com/raw/whLr21ZA"
expData.df<- read.table(dataURL,header=TRUE,sep="\t",stringsAsFactors=FALSE)
expData.mat <- as.matrix(expData.df[-c(1)])
rownames(expData.mat) <- expData.df$Mol
useT.mat <- t(expData.mat)
mat_list = list(a = useT.mat)
dend_list = list(a = as.dendrogram(hclust(dist(t(mat_list[["a"]])))) )
col_fun = colorRamp2(breaks= c(-13.288,-5.265,-6.674,-2.544,4.694,5.000), colors = c("blue4","lightblue","yellow","orange","orangered", "red"),transparency = .4)
factors = rep(letters[1], times = c( dim(useT.mat)[2] ))

circos.par(cell.padding = c(0, 0, 0, 0), gap.degree = 15)
circos.initialize(factors, xlim =cbind(c(0), table(factors)))

circos.track(ylim = c(0, 1), bg.border = NA, panel.fun = function(x, y) {
    sector.index = CELL_META$sector.index
    m = mat_list[[sector.index]]
    dend = dend_list[[sector.index]]

    m2 = m[, order.dendrogram(dend)]
    col_mat = col_fun(m2)
    nr = nrow(m2)
    nc = ncol(m2)
    for(i in 1:nr) {
        circos.rect(1:nc - 1, rep(nr - i, nc), 
            1:nc, rep(nr - i + 1, nc), 
            border = col_mat[i, ], col = col_mat[i, ])
    }
})
#Dendrogram
max_height = max(sapply(dend_list, function(x) attr(x, "height")))
circos.track(ylim = c(0, max_height), bg.border = NA, track.height = 0.3, 
    panel.fun = function(x, y) {

        sector.index = get.cell.meta.data("sector.index")
        dend = dend_list[[sector.index]]
        circos.dendrogram(dend, max_height = max_height)
})
circos.clear()

I'm having two issues while plotting the data: enter image description here

  1. Part of the figure is going outside of the plotting area on top and bottom.

  2. I don't know how to put row and column labels in the figure

can anyone help in solving these two issues?

Thanks

Solution

  • You can change the y limit of each track to match plot content, then the figure is not outside of plotting area. You can add row labels using the barplots example from circlize manual; you can add column labels by creating an extra track outside that contains only labels. This you can also roughly copy the phylogenetic tree example from the manual. Both of them are in the same Chapter, Chapter 5. Using the code you provided with some modification, an example would be the following:

    dataURL <- "https://pastebin.com/raw/whLr21ZA"
expData.df<- read.table(dataURL,header=TRUE,sep="\t",stringsAsFactors=FALSE)
expData.mat <- as.matrix(expData.df[-c(1)])
rownames(expData.mat) <- expData.df$Mol
useT.mat <- t(expData.mat)
mat_list = useT.mat #changed to fit 1 heatmap
dend_list = as.dendrogram(hclust(dist(t(mat_list)))) #changed to calculate for 1 matrix
col_fun = colorRamp2(breaks= c(-13.288,-5.265,-6.674,-2.544,4.694,5.000), 
colors = c("blue4","lightblue","yellow","orange","orangered", "red")) 
#removed transparency so easier to save in EPS, very optional
#excluded 'factor' as there is only 1 heatmap

circos.par("start.degree" = 90,cell.padding = c(0, 0, 0, 0), gap.degree = 15) 
circos.initialize("a", xlim =c(0,292)) #changed to 1 heatmap setting
#adding new track for column label
circos.track(ylim = c(0, 1), bg.border = NA, track.height = 0.05, 
panel.fun = function(x, y) {
    for(i in seq_len(ncol(useT.mat))) {
        circos.text(i-0.5, 0, colnames(useT.mat)[order.dendrogram(dend_list)][i], adj = c(0, 0.5), 
            facing = "clockwise", niceFacing = TRUE,
         cex = 0.5)                
    }
})

circos.track(ylim = c(0, 2), bg.border = NA, panel.fun = function(x, y) {
m = mat_list 
dend = dend_list
#changed variable for 1 heatmap setting
m2 = m[, order.dendrogram(dend)]
col_mat = col_fun(m2)
nr = nrow(m2)
nc = ncol(m2)
for(i in 1:nr) {
    circos.rect(1:nc - 1, rep(nr - i, nc), 
        1:nc, rep(nr - i + 1, nc), 
        border = col_mat[i, ], col = col_mat[i, ])
}
#adding row label
circos.text(rep(1, 2), 1:2, 
        rownames(useT.mat), 
        facing = "downward", adj = c(1.45, 1.1), cex = 0.7) 

})
#Dendrogram
max_height = attr(dend_list, "height") #changed for 1 dendrogram setting
circos.track(ylim = c(0, max_height), bg.border = NA, track.height = 0.3, 
panel.fun = function(x, y) {
    dend = dend_list
    circos.dendrogram(dend, max_height = max_height)
})
circos.clear()

#adding legend key
library(ComplexHeatmap)
lgd_links = Legend(at=c(-15,-5,0,5),col_fun = col_fun, 
title_position = "topleft", title = "Value", direction = "horizontal")
draw(lgd_links, x = unit(1, "npc") - unit(2, "mm"), y = unit(4, "mm"), 
just = c("right", "bottom"))

    (example figure link: https://drive.google.com/file/d/1doq7jBhuUn7g795gqFjYjux90vZIyHA8/view)

    enter image description here