circos.heatmap {circlize}

Make circular heatmaps

Description

Make circular heatmaps

Usage

circos.heatmap(mat, split = NULL, col, na.col = "grey",
    cell.border = NA, cell.lty = 1, cell.lwd = 1,
    bg.border = NA, bg.lty = par("lty"), bg.lwd = par("lwd"),
    ignore.white = is.na(cell.border),
    cluster = TRUE, clustering.method = "complete", distance.method = "euclidean",
    dend.callback = function(dend, m, si) reorder(dend, rowMeans(m)),
    dend.side = c("none", "outside", "inside"), dend.track.height = 0.1,
    rownames.side = c("none", "outside", "inside"), rownames.cex = 0.5,
    rownames.font = par("font"), rownames.col = "black",
    show.sector.labels = FALSE, cell_width = rep(1, nrow(mat)), ...)

Arguments

mat

A matrix or a vector. The vector is transformed as a one-column matrix.

split

A categorical variable. It splits the matrix into a list of matrices.

col

If the values in the matrices are continuous, the color should be a color mapping generated by colorRamp2. If the values are characters, the color should be a named color vector.

na.col

Color for NA values.

cell.border

Border color of cells. A single scalar.

cell.lty

Line type of cell borders. A single scalar.

cell.lwd

Line width of cell borders. A single scalar.

bg.border

Color for background border.

bg.lty

Line type of the background border.

bg.lwd

Line width of the background border.

ignore.white

Whether to draw the white color?

cluster

whether to apply clustering on rows. The value can also be a dendrogram/hclust object or other objects that can be converted to with as.dendrogram.

clustering.method

Clustering method, pass to hclust.

distance.method

Distance method, pass to dist.

dend.callback

A callback function that is applied to the dendrogram in every sector.

dend.side

Side of the dendrograms relative to the heatmap track.

dend.track.height

Track height of the dendrograms.

rownames.side

Side of the row names relative to the heatmap track.

rownames.cex

Cex of row names.

rownames.font

Font of row names.

rownames.col

Color of row names.

show.sector.labels

Whether to show sector labels.

cell_width

Relative widths of heatmap cells.

...

Pass to circos.track which draws the heatmap track.

See Also

https://jokergoo.github.io/2020/05/21/make-circular-heatmaps/

Examples

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)
spilt = factor(split, levels = letters[1:5])
col_fun1 = colorRamp2(c(-2, 0, 2), c("blue", "white", "red"))
circos.heatmap(mat1, split = split, col = col_fun1)
circos.clear()