GenotypeSimilarityHeatmap: Genotype similarity heatmap

In nbroguiere/burgertools: Collection of tools extending the functionality of Seurat

Genotype similarity heatmap

Description

Plot a heatmap of the similarity between the various genotypes in a genotype object.

Usage

GenotypeSimilarityHeatmap(
  genotypes,
  key.title = "Fraction of \nmatching variants",
  limits = NULL,
  plot_method = "plotly",
  colors = viridis::viridis(n = 256, alpha = 1, begin = 0, end = 1, option = "viridis"),
  ...
)

Arguments

genotypes	genotype object, contains several genotypes to be compared on the heatmap.
key.title	character(1), the legend/key. Default: "Fraction of matching variants"
limits	numeric(2), the limits of the color scale (typically c(0,1), which are the extremes values similarities could take), or NULL for min/max in current data.
plot_method	"plotly" or "ggplot". Default "plotly"
colors	a color palette, default viridis.
...	other graphic parameters passed on to heatmaply.

Details

The similarity is defined as the fraction of matching variants, i.e. the number of identical variants divided by the number of variants which are simultaneously called in both genotypes being compared.

Value

A heatmaply plot.

Examples

GenotypeSimilarityHeatmap(MyGenotypeObject)

nbroguiere/burgertools documentation built on Jan. 30, 2024, 3:48 a.m.