make_enriched_heatmap_list: Create a HeatmapList from parcutils_chip.
In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

make_enriched_heatmap_list

R Documentation

Create a HeatmapList from parcutils_chip.

Description

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()`.