Package 'crisprViz'

Title: Visualization Functions for CRISPR gRNAs
Description: Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.
Authors: Jean-Philippe Fortin [aut, cre], Luke Hoberecht [aut]
Maintainer: Jean-Philippe Fortin <[email protected]>
License: MIT + file LICENSE
Version: 1.9.0
Built: 2024-11-29 08:55:46 UTC
Source: https://github.com/bioc/crisprViz

Help Index

CAGE peak annotation from AnnotationHub

Description

A sample of CAGE peak annotation from AnnotationHub (ascension number AH5084), lifted over to hg38.

Usage

data(cage, package="crisprViz")

Format

A GRanges object.

Example GuideSet targeting the human LTN1 gene.

Description

An example GuideSet object targeting the CDS of the human LTN1 gene. Generated using the AsCas12a CRISPR nuclease, the genome sequence from the BSgenome.Hsapiens.UCSC.hg38 package, and the gene model from txdb_human in the crisprDesignData package (Ensembl release 104).

Usage

data(cas12aGuideSet, package="crisprViz")

Format

A GuideSet object.

Example GuideSet targeting the human LTN1 gene.

Description

An example GuideSet object targeting the CDS of the human LTN1 gene. Generated using the SpCas9 CRISPR nuclease, the genome sequence from the BSgenome.Hsapiens.UCSC.hg38 package, and the gene model from txdb_human in the crisprDesignData package (Ensembl release 104).

Usage

data(cas9GuideSet, package="crisprViz")

Format

A GuideSet object.

DNase I hypersensitive site annotation from AnnotationHub

Description

A sample of DNase I hypersensitive site annotation from AnnotationHub (ascension number AH30743), lifted over to hg38.

Usage

data(dnase, package="crisprViz")

Format

A GRanges object.

CompressedGRangesList describing the human GPR21 gene.

Description

A CompressedGRangesList object describing the gene model of the human GPR21 gene. Coordinates were subset from txdb_human in the crisprDesignData package (Ensembl release 104).

Usage

data(gpr21GeneModel, package="crisprViz")

Format

A CompressedGRangesList object.

Example GuideSet targeting the human GPR21 gene.

Description

An example GuideSet object targeting a section of the CDS of the human GPR21 gene. Generated using the BE4max CRISPR nuclease, the genome sequence from the BSgenome.Hsapiens.UCSC.hg38 package, and the gene model from txdb_human in the crisprDesignData package (Ensembl release 104).

Usage

data(gpr21GuideSet, package="crisprViz")

Format

A GuideSet object.

CompressedGRangesList describing the human KRAS gene.

Description

A CompressedGRangesList object describing the gene model of the human KRAS gene. Coordinates were subset from txdb_human in the crisprDesignData package (Ensembl release 104).

Usage

data(krasGeneModel, package="crisprViz")

Format

A CompressedGRangesList object.

Example GuideSet targeting the human KRAS gene.

Description

An example GuideSet object targeting the CDS of the human KRAS gene. Generated using the SpCas9 CRISPR nuclease, the genome sequence from the BSgenome.Hsapiens.UCSC.hg38 package, and the gene model from txdb_human in the crisprDesignData package (Ensembl release 104).

Usage

data(krasGuideSet, package="crisprViz")

Format

A GuideSet object.

CompressedGRangesList describing the human LTN1 gene.

Description

A CompressedGRangesList object describing the gene model of the human LTN1 gene. Coordinates were subset from txdb_human in the crisprDesignData package (Ensembl release 104).

Usage

data(ltn1GeneModel, package="crisprViz")

Format

A CompressedGRangesList object.

CompressedGRangesList describing the human MMP7 gene.

Description

A CompressedGRangesList object describing the gene model of the human MMP7 gene. Coordinates were subset from txdb_human in the crisprDesignData package (Ensembl release 104).

Usage

data(mmp7GeneModel, package="crisprViz")

Format

A CompressedGRangesList object.

Example GuideSet targeting the human MMP7 gene.

Description

An example GuideSet object targeting the promoter region of the human MMP7 gene. Generated using the SpCas9 CRISPR nuclease, the genome sequence from the BSgenome.Hsapiens.UCSC.hg38 package, and the gene model from tss_human in the crisprDesignData package (Ensembl release 104).

Usage

data(mmp7GuideSet, package="crisprViz")

Format

A GuideSet object.

Plotting a GuideSet and other genomic annotations

Description

Function to plot guide targets stored in a GuideSet object in a gene browser view supported by Gviz. Target gene isoforms and other genomic annotation, along with the target chromosome ideogram and sequence, may also be added, permitting a comprehensive visualization of the genomic context around the target protospacer sequences.

Usage

plotGuideSet(
  x,
  geneModel = NULL,
  targetGene = NULL,
  annotations = list(),
  from = NULL,
  to = NULL,
  extend.left = 0,
  extend.right = 0,
  margin = 1,
  includeIdeogram = TRUE,
  bands = NULL,
  guideStacking = "squish",
  bsgenome = NULL,
  pamSiteOnly = FALSE,
  showGuideLabels = TRUE,
  onTargetScore = NULL,
  includeSNPTrack = TRUE,
  gcWindow = NULL
)

Arguments

x

A GuideSet object.
geneModel

A TxDb object or a GRangesList object obtained using TxDb2GRangesList.
targetGene

String specifying the gene symbol or Ensembl ID of the gene to plot.
annotations

A named (optional) list of genomic annotations as GRanges to plot. Provided names are displayed as track titles.
from, to

Numeric value giving the genomic coordinate range to plot; see plotTracks.
extend.left, extend.right

Numeric value giving the length in bases to extend the plotting range; see plotTracks.
margin

A numeric value that sets the margin of the plotting range with respect to the range of x. The value is a ratio of the width of x considered as a single range, with a value of 1 (default) extending the plotting window by the same distance as that between min(start(x)) and max(end(x)). Only works for the respective side of the plot if either from or to are NULL.
includeIdeogram

Logical; whether to include an IdeogramTrack in the plot.
bands

A data.frame of cytoband information for the target genome required for ideogram plotting; see IdeogramTrack.
guideStacking

Character string specifying how to stack guides. Options are squish, dense, hide (see GeneRegionTrack), or NA to have each guide occupy a separate track.
bsgenome

A BSgenome object; used to generate SequenceTrack and GC content DataTrack.
pamSiteOnly

Whether to plot only the PAM site in representing guides, or plot the full guide and PAM sequence (default).
showGuideLabels

Logical; whether to show labels for individual guides.
onTargetScore

Optional column name in mcols(x) of on-target scores. Applies a color scheme to the guide track based on on-target scores, with light gray corresponding to 0 and dark blue corresponding to 1.
includeSNPTrack

Logical; whether to include an AnnotationTrack for SNPs if such annotation exists in x.
gcWindow

If not NULL, a numeric value specifying the distance from a given base for which to establish a window for calculating GC content at that base. These values are then added to the plot in a DataTrack.

Value

A Gviz plot; see plotTracks.

Author(s)

Luke Hoberecht

See Also

plotMultipleGuideSets for plotting multiple GuideSet objects together.

Examples

if (interactive()){
data(krasGuideSet, package="crisprViz")
data(krasGeneModel, package="crisprViz")
plotGuideSet(krasGuideSet[1:4],
             geneModel=krasGeneModel,
             targetGene="KRAS")
}

Plotting a GuideSet and other genomic annotation

Description

Function to plot guide targets stored in multiple GuideSet objects in a gene browser view supported by Gviz. Target gene isoforms and other genomic annotation, along with the target chromosome ideogram and sequence, may also be added, permitting a comprehensive visualization of the genomic context targeted by spacers in GuideSet objects.

Usage

plotMultipleGuideSets(
  x,
  geneModel = NULL,
  targetGene = NULL,
  annotations = list(),
  from = NULL,
  to = NULL,
  extend.left = 0,
  extend.right = 0,
  margin = 1,
  includeIdeogram = TRUE,
  bands = NULL,
  bsgenome = NULL,
  onTargetScores = NULL,
  includeSNPTrack = TRUE,
  gcWindow = NULL
)

Arguments

x

A named (optional) list of GuideSet objects. List names are displayed as track titles.
geneModel

A TxDb object or a GRangesList object obtained using TxDb2GRangesList.
targetGene

A character string giving the gene symbol or Ensembl ID of the gene to plot.
annotations

A named (optional) list of genomic annotations as GRanges to plot. Provided names are displayed as track titles.
from, to

Numeric value giving the genomic coordinate range to plot; see plotTracks.
extend.left, extend.right

Numeric value giving the length in bases to extend the plotting range; see plotTracks.
margin

A numeric value that sets the margin of the plotting range with respect to the range of x. The value is a ratio of the width of x considered as a single range, with a value of 1 (default) extending the plotting window by the same distance as that between min(start(x)) and max(end(x)). Only works for the respective side of the plot if either from or to are NULL.
includeIdeogram

Logical; whether to include an IdeogramTrack in the plot.
bands

A data.frame of cytoband information for the target genome required for ideogram plotting; see IdeogramTrack.
bsgenome

A BSgenome object; used to generate SequenceTrack and GC content DataTrack.
onTargetScores

Optional list of column names for each element in x of on-target scores. Applies a color scheme to the guide track based on on-target scores, with light gray corresponding to 0 and dark blue corresponding to 1.
includeSNPTrack

Logical; whether to include an AnnotationTrack for SNPs if such annotation exists in x.
gcWindow

If not NULL, a numeric value specifying the distance from a given base for which to establish a window for calculating GC content at that base. These values are then added to the plot in a DataTrack.

Value

A Gviz plot; see plotTracks.

Author(s)

Luke Hoberecht, Jean-Philippe Fortin

See Also

plotGuideSet

Examples

if (interactive()){
library(BSgenome.Hsapiens.UCSC.hg38)
data(cas9GuideSet, package="crisprViz")
data(cas12aGuideSet, package="crisprViz")
data(ltn1GeneModel, package="crisprViz")
plotMultipleGuideSets(list(SpCas9=cas9GuideSet, AsCas12a=cas12aGuideSet),
                      geneModel=ltn1GeneModel,
                      targetGene="LTN1",
                      bsgenome=BSgenome.Hsapiens.UCSC.hg38,
                      margin=0.2,
                      gcWindow=10)
}

Subset of repeat elements for hg38.

Description

A GRanges object describing a subset of repeat elements for the hg38 genome. Coordinates were subset from gr.repeats.hg38 in the crisprDesignData package.

Usage

data(repeats, package="crisprViz")

Format

A GRanges object.