circos.heatmap: Make circular heatmaps

In jokergoo/circlize: Circular Visualization

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()

jokergoo/circlize documentation built on Nov. 17, 2023, 11:32 a.m.