Object generator for S4 class ccHeatmap — ccHeatmap • circlizePlus

Object ccHeatmap will call the function circlize::circos.heatmap while drawing.

Usage

ccHeatmap(
  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.

Value

Object ccHeatmap

Examples

library(circlizePlus)
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"))
ccHeatmap(mat = mat1, split = split, col = col_fun1)