PlotPerturbScore: Function to plot perturbation score distributions.

In Seurat: Tools for Single Cell Genomics

Function to plot perturbation score distributions.

Description

Density plots to visualize perturbation scores calculated from RunMixscape function.

Usage

PlotPerturbScore(
  object,
  target.gene.class = "gene",
  target.gene.ident = NULL,
  mixscape.class = "mixscape_class",
  col = "orange2",
  split.by = NULL,
  before.mixscape = FALSE,
  prtb.type = "KO"
)

Arguments

object	An object of class Seurat.
target.gene.class	meta data column specifying all target gene names in the experiment.
target.gene.ident	Target gene name to visualize perturbation scores for.
mixscape.class	meta data column specifying mixscape classifications.
col	Specify color of target gene class or knockout cell class. For control non-targeting and non-perturbed cells, colors are set to different shades of grey.
split.by	For datasets with more than one cell type. Set equal TRUE to visualize perturbation scores for each cell type separately.
before.mixscape	Option to split densities based on mixscape classification (default) or original target gene classification. Default is set to NULL and plots cells by original class ID.
prtb.type	specify type of CRISPR perturbation expected for labeling mixscape classifications. Default is KO.

Value

A ggplot object.

Seurat documentation built on Nov. 18, 2023, 1:10 a.m.