plot.synthetic_lethal: plot.synthetic_lethal

In alex-kalinka-cruk/crispRutils: Tools for working with CRISPR data.

Description

Plot of Treatment-vs-plasmid against Control-vs-plasmid (logFC scatterplots), and volcano plot of Treatment-vs-Control. New essential genes and lost essential genes are highlighted, but only new essential genes are annotated with gene names.

Usage

## S3 method for class 'synthetic_lethal'
plot(
  x,
  type,
  remove_multimappers,
  label_hits = TRUE,
  library_name = NULL,
  library_type = NULL,
  library_annotation_version = NULL,
  ...
)

Arguments

x	An object of class 'synthetic_lethal'.
type	Either 'plasmid' or 'treat'.
remove_multimappers	Logical, whether to remove genes that have at least 1 guide that is a multi-mapper. Issues a warning if any of the genes appear in the new or lost essential groups.
label_hits	Logical, whether to add gene names to plot, or simply colour them. Defaults to 'TRUE'.
library_name	Name of the library, e.g. "yusa_v3_human" - must match naming conventions used in the AZ-CRUK reference data repo.
library_type	One of "n" (knock-out), "a" (activation), or "i" (interference).
library_annotation_version	An integer giving the annotation version of the library.
...	Other arguments to pass to 'plot'.

Value

Renders a plot in the console.

Author(s)

Alex T. Kalinka [e-mail]

alex-kalinka-cruk/crispRutils documentation built on March 13, 2021, 7:52 p.m.