Create a HeatmapList from parcutils_chip.

Usage

make_enriched_heatmap_list(
  x,
  cluster_targets_by_rpm = TRUE,
  cluster_by = NULL,
  n_clust = 2,
  cluster_rows = FALSE,
  heatmap_columns = NULL,
  heatmap_column_title = NULL,
  heatmap_pos_line = FALSE,
  heatmap_pos_line_gp = grid::gpar(lty = 2),
  heatmap_color_palette = "Oranges",
  reverse_palette = FALSE,
  heatmap_scale = c(0, 0.5, 1),
  heatmap_top_annotations = NULL,
  heatmap_axis_name = c("-3KB", "Summit", "+3KB"),
  heatmap_axis_name_rot = 0,
  heatmap_axis_name_gp = gpar(fontsize = 10),
  heatmap_border = TRUE
)

Arguments

x: an object of the class parcutils_chip.
cluster_targets_by_rpm: logical, denoting whether to cluster targets by RPM value.
cluster_by: NULL (default) or character vector denoting RPM columns to be used for clustering.
n_clust: a numeric, default 2, denoting number of clusters for kmeans clustering.
cluster_rows: logical, default FALSE, denoting whether to cluster rows using default clustering. This must be always false as kmeans is implimented.
heatmap_columns: NULL (default, all columns) or character vector denoting columns to be displayed in the heatmap.
heatmap_column_title: NULL (default) or character vector denoting title for each heatmap column.
heatmap_pos_line: logical, default FALSE, internally passed to pos_line argument of EnrichedHeatmap::EnrichedHeatmap().
heatmap_pos_line_gp: logical, default FALSE, internally passed to pos_line_gp argument of EnrichedHeatmap::EnrichedHeatmap().
heatmap_color_palette: a character vector denoting a valid color palette(s) from grDevices::hcl.pals(). More than one will be used to color each heatmap. Default Oranges.
reverse_palette: Logical, FALSE, denoting whether to reverse the color palette.
heatmap_scale: a numeric vector denoting a heatmap scale. Default (0,0.5,1).
heatmap_top_annotations: internally passed to top_annotations argument of EnrichedHeatmap::EnrichedHeatmap().
heatmap_axis_name: internally passed to axis_name argument of EnrichedHeatmap::EnrichedHeatmap().
heatmap_axis_name_rot: internally passed to axis_name_rot argument of EnrichedHeatmap::EnrichedHeatmap().
heatmap_axis_name_gp: internally passed to axis_name_gp argument of EnrichedHeatmap::EnrichedHeatmap().
heatmap_border: internally passed to border argument of EnrichedHeatmap::EnrichedHeatmap().

Value

a HeatmapList.

Examples

if (FALSE) {
}