heatmap_column_order: Return Heatmap column order from ComplexHeatmap heatmap...

In jmw86069/jamba: Jam Base Methods

Return Heatmap column order from ComplexHeatmap heatmap object

Description

Return Heatmap column order from ComplexHeatmap heatmap object

Usage

heatmap_column_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 colnames 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 colnames() when present, or integer column index values when there are no colnames(). If heatmap column_labels are defined, they are returned as names().

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

Value

output depends upon the heatmap:

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

• When columns are grouped using column_split, it returns a list of vectors as described above. The list is named using the column_title labels only when there is an equal number of column labels.

See Also

Other jam heatmap functions: cell_fun_label(), heatmap_row_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.