Make circular heatmaps
Make circular heatmaps
circos.heatmap(mat, split = NULL, col, na.col = "grey",
bg.border = NA, bg.lty = par("lty"), bg.lwd = par("lwd"), ignore.white = TRUE,
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)), ...)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 |
na.col |
Color for |
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 |
clustering.method |
Clustering method, pass to |
distance.method |
Distance method, pass to |
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 |
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()Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.