HeatmapVoi: HeatmapVoi

In CostaLab/sigurd: Single cell Genotyping Using RNA Data

HeatmapVoi

Description

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

CostaLab/sigurd documentation built on Feb. 10, 2025, 11:08 p.m.