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_colors = circlize::colorRamp2(breaks = c(0, 0.5, 1), colors = c("#fee6ce",
"#e6550d", "#E31A1C")),
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 weather 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 weather to cluster rows using default clustering. This must be always false as kmeans is implimented.
- heatmap_columns
NULL (default) 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 ofEnrichedHeatmap::EnrichedHeatmap()
.- heatmap_pos_line_gp
logical, default FALSE, internally passed to
pos_line_gp
argument ofEnrichedHeatmap::EnrichedHeatmap()
.- heatmap_colors
internally passed to
col
argument ofEnrichedHeatmap::EnrichedHeatmap()
. Defaultcirclize::colorRamp2(breaks = c(0,0.5,1),colors = c('#fee6ce','#e6550d','#E31A1C'))
.- heatmap_top_annotations
internally passed to
top_annotations
argument ofEnrichedHeatmap::EnrichedHeatmap()
.- heatmap_axis_name
internally passed to
axis_name
argument ofEnrichedHeatmap::EnrichedHeatmap()
.- heatmap_axis_name_rot
internally passed to
axis_name_rot
argument ofEnrichedHeatmap::EnrichedHeatmap()
.- heatmap_axis_name_gp
internally passed to
axis_name_gp
argument ofEnrichedHeatmap::EnrichedHeatmap()
.- heatmap_border
internally passed to
border
argument ofEnrichedHeatmap::EnrichedHeatmap()
.