AnnotatedVariableFeaturePlot: Annotated variable features plot

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

Annotated variable features plot

Description

This function displays a variable feature plot with feature annotations.

Usage

AnnotatedVariableFeaturePlot(
  object,
  which.labels = NA,
  pt.size = 1,
  text.size = 2.5,
  log = NULL,
  xnudge = 0,
  ynudge = 0,
  colors = c("Black", "Cyan"),
  selection.method = NULL,
  assay = NULL
)

Arguments

object	Seurat object. Must contain nFeature_RNA and percent.mito metadata columns, or the x and y plot parameters must be changed accordingly to plot other QC info otherwise.
which.labels	Number of most variable features to label, or list of variable features to label. If NA, label all the variable features (Default: NA).
pt.size	Size of the points on the plot (Default: 1)
text.size	Size of the feature annotations (Default: 2.5)
log	Plot the x-axis on log scale
xnudge	Offset in x on label position (Default: 0)
ynudge	Offset in y on label position (Default: 0)
colors	Colors to specify non-variable/variable status (Default: c("Black","Cyan")).
selection.method	Which method to pull (refer to ?Seurat::VariableFeaturePlot()).
assay	Assay to pull variable features from

Value

A ggplot object.

Examples

SeuratObject <- FindVariableFeatures(SeuratObject)
# Annotate all variable features:
AnnotatedVariableFeaturePlot(SeuratObject)
# Annotate user-defined genes:
AnnotatedVariableFeaturePlot(SeuratObject,c("OLFM4","LGR5","CD44","GAPDH"))
AnnotatedVariableFeaturePlot(SeuratObject,500)

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