heatmap_row_order: Return Heatmap row order from ComplexHeatmap heatmap object

In jmw86069/jamba: Jam Base Methods

Return Heatmap row order from ComplexHeatmap heatmap object

Description

Return Heatmap row order from ComplexHeatmap heatmap object

Usage

heatmap_row_order(hm)

Arguments

hm	Heatmap or HeatmapList object as defined by the Bioconductor package via ComplexHeatmap::Heatmap().

Details

This function is a helpful utility to return the fully qualified list of rownames in a ComplexHeatmap::Heatmap object.

The core intention is for the output to be usable with the original data matrix used in the heatmap. Therefore, the vector values are rownames() when present, or integer row index values when there are no rownames(). If heatmap row_labels are defined, they are returned as names().

Note that names() are assigned inside try() to allow the case where row_labels, or row_title labels cannot be coerced to character values, for example using gridtext for markdown formatting.

Final note: It is best practice to draw the heatmap first with ComplexHeatmap::draw() then store the output in a new object. This step creates the definitive clustering and therefore the row order is absolutely final, not subject to potential randomness during clustering.

Value

output depends upon the heatmap:

• When heatmap rows are grouped using row_split, and when the data matrix contains rownames, returns a character vector of rownames in the order they appear in the heatmap. When there are no rownames, integer row index values are returned. If the heatmap has row labels, they are returned as vector names.

• When rows are grouped using row_split, it returns a list of vectors as described above. The list is named using the row_title labels only when there is an equal number of row labels.

See Also

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

Examples

if (check_pkg_installed("ComplexHeatmap")) {
   set.seed(123);

   mat <- matrix(rnorm(18 * 24),
      ncol=24);
   rownames(mat) <- paste0("row", seq_len(18))
   colnames(mat) <- paste0("column", seq_len(24))

   # obtaining row order first causes a warning message
   hm1 <- ComplexHeatmap::Heatmap(mat);

   # best practice is to draw() and store output in an object
   # to ensure the row orders are absolutely fixed
   hm1_drawn <- ComplexHeatmap::draw(hm1);
   heatmap_row_order(hm1_drawn)
   heatmap_column_order(hm1_drawn)

}

jmw86069/jamba documentation built on March 26, 2024, 5:26 a.m.