CNV heatmap across samples

Plot per-window copy-number estimates stored in a qseaSet as a heatmap using ComplexHeatmap. Each column is a sample; rows are genome windows.

plotCNVheatmap(
  qseaSet,
  sampleAnnotation = NULL,
  annotationColors = NA,
  clusterRows = TRUE
)

Arguments

qseaSet

qseaSet. Input object containing per-window CNV tracks (e.g., created by addHMMcopyCNV() or qsea::addCNV()).

sampleAnnotation

tidyselect specification, character(), or NULL. Sample-table columns to display as column annotations (e.g., c("tumour","type") or bare helpers tumour, type). Default: NULL.

annotationColors

list or NA. Optional mapping of levels → colours to override auto palettes, e.g. list(tumour = c(Tumour = "firebrick4", Normal = "blue")). Default: NA.

clusterRows

logical(1). Cluster rows (windows) before plotting. Default: TRUE.

Value

Draws a heatmap on the active device and (invisibly) returns the underlying ComplexHeatmap object for further composition with draw.

Details

Assumes CNV values are available per window and sample. Rows are windows (typically in genomic order if clusterRows = FALSE), columns are samples. Sample annotations (and optional colours) are added when sampleAnnotation and annotationColors are provided.

See also

addHMMcopyCNV(), runHMMcopy(), Heatmap, qsea::addCNV()

Other CNV: addHMMcopyCNV(), removeCNV(), runHMMCopy()

Examples

data(exampleTumourNormal, package = "mesa")

# Basic CNV heatmap with sample annotations
exampleTumourNormal %>%
    plotCNVheatmap(sampleAnnotation = c(tumour, type))


# Custom annotation colours; disable row clustering
exampleTumourNormal %>%
    plotCNVheatmap(
        sampleAnnotation = tumour,
        annotationColors = list(
            tumour = c(Tumour = "firebrick4", Normal = "blue")
        ),
        clusterRows = FALSE
    )