VariantPlot: Plots variants

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

Plots variants

Description

Plots variants as dot color on top of a dimensionality reduction used as x-y coordinates. By default, reference allele is blue, alternate allele is red, and heterozygous is purple.

Usage

VariantPlot(
  object,
  variants,
  reduction = NA,
  dims = c(1, 2),
  pt.size = 1,
  n.rows = NA,
  assay = "VAR",
  colors = c("lightgrey", "blue", "red", "purple"),
  order = T
)

Arguments

object	Seurat object.
variants	character(n). The name of the variant(s) to plot (as point color)
reduction	character(1). The name of the dimensionality reduction that should be used as xy axis. If NA, will use umap, or tsne, or pca, in this order. Default: NA.
dims	numeric(2). The dimensions within the dimensionality reduction that should be used as xy axis. Default: c(1,2).
pt.size	numeric(1).The point size. Default: 1.
n.rows	numeric(1).The number of rows in the plot grid. NA for automatic smart choice. Default: NA.
assay	numeric(1). The assay from which the variant calls (in vartrix conventions) should be pulled. Default: "VAR".
colors	character(n). Four colors, that will be used respectively for: no call, ref/ref, alt/alt, ref/alt calls.
order	logical(1). Should the cells be ordered, with no call at the bottom and heterozygous on top, before plotting. Default: T.

Value

Returns a cowplot grid of plots

Examples

VariantPlot(MySeuratObject, "KRAS-12-G/D-MODERATE-chr12-25245350-C-T")
VariantPlot(MySeuratObject, VariableFeatures(MySeuratObject[["VAR"]])[1:9], reduction="mds", dims=c(1,3))

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