InformativeVariantPlot: Plot the informative variants with annotations

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

Plot the informative variants with annotations

Description

Plots the excess entropy vs coverage of the variants, highlighting in color the informative variants. Optionally, can label all or only informative variants, or the variants having a minimal impact or present in a minimal percent of TCGA patients for the relevant cohort, or a combination thereof.

Usage

InformativeVariantPlot(
  object,
  do.label = T,
  label.column = "variants",
  label.only.informative = T,
  min.impact = NA,
  min.tcga.percent = NA,
  check.overlap = T,
  pt.size = 1,
  text.size = 3.5,
  colors.use = c("grey", "#8888FF", "red"),
  log.scale = F,
  min.entropy = 0.001,
  assay = "VAR"
)

Arguments

object	A seurat or genotype object on which FindInformativeVariants() has been computed.
do.label	logical(1). Should variants be labeled (Default: TRUE).
label.column	character(1). Which metadata column should be used as labels (Default: variants).
label.only.informative	logical(1). Should the labels only be for informative variants (Default: TRUE).
min.impact	character(1). Label only variants which have a predicted impact more than "LOW", "MODERATE", or "HIGH". NA to label all (Default:NA).
min.tcga.percent	character(1). Label only variants which concern genes mutated in more than a certain percent of TCGA patients in the cohort used for genotype annotation. Requires a tcga_percent column to be present in the genotype object.
check.overlap	logical(1). Should overlapping labels be omitted (Default: TRUE).
pt.size	numeric(1). The point size (Default: 1).
text.size	numeric(1). The text size (Default:3.5).
colors.use	character(3). The colors for other variants, informative variants, and high impact / high tcga percent variants, in this order (Default: c("grey","#8888FF","red")).
log.scale	logical(1). Should the axis be switched to log scale (Default: FALSE).
min.entropy	numeric(1). Minimal excess_entropy value for variants to be represented by a dot in the graph. Values above 0, even small, greatly speed up rendering without noticeably changing the result, if many very low informative variants are present. More critical when using log scale, as low entropy variants are then visible (Default:1e-3).
assay	character(1). If the object is a seurat object, which assay contains the consensus variant data (Default: "VAR").

Value

Returns a ggplot

Examples

InformativeVariantPlot(MyObject,label.column = "summary") # Other labels that can be interesting: symbol, summary, short_description.. see also colnames(MyGenotypes@metadata)
InformativeVariantPlot(MyObject,label.column = "summary",min.impact = "MODERATE") # Only label the variants that have a predicted impact more than moderate
InformativeVariantPlot(MyObject,label.column = "summary",min.impact = "MODERATE",min.tcga.percent = 1,label.only.informative=F,log.scale = T) # Add the restriction to only label above a minimal tcga percent. The results are few, so label even non-informative variants, and activate log scale to see better the low coverage variants.

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