Return Heatmap row order from ComplexHeatmap heatmap object
heatmap_row_order(hm, which_heatmap = NULL)
hm: Heatmap or HeatmapList object as defined by the Bioconductor package via ComplexHeatmap::Heatmap().which_heatmap: integer, default NULL, used when the input is a HeatmapList with multiple heatmaps.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.
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.
# See heatmap_column_order() for examples
Other jam heatmap functions: cell_fun_label(), heatmap_column_order()