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R
Seurat

PlotPerturbScore

Function to plot perturbation score distributions.

Description

Density plots to visualize perturbation scores calculated from RunMixscape function.

Usage

PlotPerturbScore(
  object,
  target.gene.ident = NULL,
  group.by = "mixscape_class",
  col = "orange2",
  prtb.type = "KO"
)

Arguments

object

An object of class Seurat.
target.gene.ident

Class identity for cells sharing the same perturbation. Name should be the same as the one used to run mixscape.
group.by

Option to split densities based on mixscape classification. Default is set to NULL and plots cells by original class ID.
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.
prtb.type

specify type of CRISPR perturbation expected for labeling mixscape classifications. Default is KO.

Value

A ggplot object.

Seurat

Tools for Single Cell Genomics

v4.0.1
GPL-3 | file LICENSE
Authors
Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]
Initial release
2021-03-17

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