cell_fun_label function

ComplexHeatmap cell function to label heatmap cells

cell_fun_label(
  m,
  prefix = "",
  suffix = "",
  cex = 1,
  col_hm = NULL,
  outline = FALSE,
  abbrev = FALSE,
  show = NULL,
  rot = 0,
  sep = "\n",
  verbose = FALSE,
  ...
)

Arguments

• m: numeric matrix or list of matrix objects. The first matrix object must be numeric and compatible with the color function col_hm.
• prefix, suffix: character vectors that define a prefix and suffix for each value in m for each cell.
• cex: numeric adjustment for the fontsize used for each label, which is multiplied by the default fontsize=10 to determine the fontsize.
• col_hm: function as returned by circlize::colorRamp2() which should be the same function used to create the heatmap
• outline: logical indicating whether to draw an outline around each heatmap cell
• abbrev: logical indicating whether numeric values should be abbreviated using jamba::asSize(..., kiloSize=1000) which effectively reduces large numbers to k for thousands, M for millions (M for Mega), G for billions (G for Giga), etc.
• show: integer used when m is supplied as a list of matrices, in which case show is used to define which values should be used as cell labels. By default, all matrices are used.
• rot: numeric value used to rotate cell label text, default 0 is horizontal.
• sep: character string, default "\n" newline, used when there are multiple labels per cell, which also requires m as a list, and show is NULL or has multiple values.
• verbose: logical indicating whether to print verbose output, specifically printing label information for position (1, 1). This output will only be seen when rendering or building the Heatmap object.
• ...: additional arguments are ignored.

Returns

function sufficient to use as input to ComplexHeatmap::Heatmap() argument cell_fun.

Details

This function serves as a convenient method to add text labels to each cell in a heatmap produced by ComplexHeatmap::Heatmap(), via the argument cell_fun.

Note that this function requires re-using the specific color function used for the heatmap in the call to ComplexHeatmap::Heatmap().

This function is slightly unique in that it allows multiple labels, if m is supplied as a list of matrix objects. In fact, some matrix objects may contain character

values with custom labels.

Cell labels are colored based upon the heatmap cell color, which is passed to jamba::setTextContrastColor() to determine whether to use light or dark text color for optimum contrast.

TODO: Option to supply a logical matrix to define a subset of cells to label, for example only labels that meet a filter criteria. Alternatively, the matrix data supplied in m can already be filtered.

TODO: Allow some matrix values that contain character data to use gridtext for custom markdown formatting. That process requires a slightly different method.

Examples

m <- matrix(stats::rnorm(16)*2, ncol=4)
colnames(m) <- LETTERS[1:4]
rownames(m) <- letters[1:4]
col_hm <- circlize::colorRamp2(breaks=(-2:2) * 2,
   colors=c("navy", "dodgerblue", "white", "tomato", "red4"))

# the heatmap can be created in one step
hm <- ComplexHeatmap::Heatmap(m,
   col=col_hm,
   heatmap_legend_param=list(
      color_bar="discrete",
      border=TRUE,
      at=-4:4),
   cell_fun=cell_fun_label(m,
      col_hm=col_hm))
ComplexHeatmap::draw(hm)

# the cell label function can be created first
cell_fun <- cell_fun_label(m,
   outline=TRUE,
   cex=1.5,
   col_hm=col_hm)
hm2 <- ComplexHeatmap::Heatmap(m,
   col=col_hm,
   cell_fun=cell_fun)
ComplexHeatmap::draw(hm2)

See Also

Other jam heatmap functions: heatmap_column_order(), heatmap_row_order()