HeatmapVoi

We plot a heatmap of a set of Variants Of Interest using the Variant Allele Frequency values of a SummarizedExperiment object.

Usage

HeatmapVoi(
  SE,
  voi,
  annotation_trait = NULL,
  column_title = NULL,
  minimum_coverage = 0,
  sort_cells = FALSE,
  remove_empty_cells = FALSE,
  minimum_allele_freq = 0,
  cluster_variants = FALSE,
  cluster_variants_distance = "euclidean",
  cluster_variants_method = "complete"
)

Arguments

SE

SummarizedExperiment object.

voi

Variants Of Interest.

annotation_trait

Cell Annotation at the bottom of the heat map.

column_title

The title of the heat map. Default = NULL

minimum_coverage

The minimum coverage per cell to be plotted.

sort_cells

Should the cells be sorted by ordering the cells according the the largest clones? FALSE uses default complete clustering with euclidean distance.

remove_empty_cells

Should cells that have a fraction of 0 for all variants be removed? Default = FALSE

minimum_allele_freq

Minimum allele frequency to include a cell.

cluster_variants

Should the variants be clustered? Default FALSE.

cluster_variants_distance

The distance for clustering the variants. Default euclidean.

cluster_variants_method

The distance for the variant clustering. Default complete