Plot copy number heatmap

Usage

cnaHeatmap(
  sce,
  assay_name = "state",
  clone_name = NULL,
  cluster_cells = FALSE,
  log2 = FALSE,
  center = FALSE,
  scale = c("none", "cells", "bins", "both"),
  label_genes = NULL,
  col_fun = NULL,
  col_clones = NULL,
  cluster_clones = FALSE,
  legend_name = assay_name,
  clust_annot = TRUE,
  verbose = TRUE,
  top_annotation = NULL,
  bulk_cn_col = NULL,
  raster_quality = 10,
  row_split = NULL,
  ...
)

cloneCnaHeatmap(
  sce,
  assay_name = "counts",
  clone_name = NULL,
  scale = c("none", "cells", "bins", "both"),
  log2 = FALSE,
  center = FALSE,
  clust_lab = TRUE,
  aggr_fun = mean,
  round = FALSE,
  ...
)

Arguments

sce: A SingleCellExperiment object
assay_name: Name of the assay to plot
clone_name: Name of clone_id column in sce object
cluster_cells: If the value is a logical, it controls whether to make cluster on rows. The value can also be a stats::hclust or a stats::dendrogram which already contains clustering. Note this will override ordering of specified clones. Check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#clustering.
log2: Logical: Log2 transform the matrix prior to plotting
center: logical: center the matrix prior to plotting
scale: One of 'cells', 'bins', 'both' or 'none'. Determines what kind of scaling is done.
label_genes: Optional: Vector of gene names to label in the heatmap. Note: overlap_genes must be run prior to labelling genes.
col_fun: Color mapping function from circlize::colorRamp2()
col_clones: Optional: A named vector (or unnamed) of clone colors.
cluster_clones: Logical: Whether or not to order the clones by clustering
legend_name: Name of the legend
clust_annot: Annotate cluster and sample labels
verbose: Logical: Message verbosity
top_annotation: Top annotation as per ComplexHeatmap::columnAnnotation()
bulk_cn_col: Name of column in rowRanges(sce) that contains bulk copy number data to plot on top of heatmap
raster_quality: Quality of raster (default: 10)
row_split: Row split for ComplexHeatmap::Heatmap()
...: Additional parameters that can be passed to ComplexHeatmap::Heatmap()
clust_lab: Cluster labels
aggr_fun: Aggregation function
round: Round pseudobulked values to integers

Value

A heatmap