crisprViz

Workflows

Standard Workflow

library(crisprViz)
library(BSgenome.Hsapiens.UCSC.hg38)
data("krasGuideSet", package="crisprViz")
data("krasGeneModel", package="crisprViz")

plotGuideSet(krasGuideSet[1:4], geneModel=krasGeneModel, targetGene="KRAS")

Inputs: A GuideSet object (krasGuideSet) and a gene model GRangesList (krasGeneModel). Outputs: A genomic track plot visualizing the gRNAs against the gene model.

Compare Multiple Guidesets

library(crisprViz)
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)

Inputs: A list of GuideSet objects for different nucleases, a gene model, and a reference BSgenome object. Outputs: A multi-track genomic plot comparing target distributions and GC content.

When to Use

• gRNA Track Visualization: Visualizing gRNA cutting locations against target genes or genomic regions using plotGuideSet.
• Nuclease Comparison: Comparing multiple GuideSet objects targeting the same region side-by-side using plotMultipleGuideSets.
• Genomic Annotations: Adding genomic annotations (e.g., repeat elements, CAGE peaks, DNase I hypersensitivity sites) to gRNA plots using the annotations argument.
• Score-Based Color Coding: Coloring gRNAs based on on-target efficiency scores (e.g., DeepHF) using the onTargetScore argument.

When NOT to Use

• Unsupported R/Bioconductor Versions: Do not use if R version is less than 4.2.0 or Bioconductor version is less than 3.16.
• gRNA Design or Scoring: Do not use for designing gRNAs or calculating scores directly (use crisprDesign and crisprScore instead).

Data Requirements

• GuideSet: A GuideSet object containing candidate gRNAs (e.g., krasGuideSet).
• Gene Model: A gene model represented as a GRangesList object (e.g., krasGeneModel).
• Reference Genome: A BSgenome object for genomic sequence visualization (e.g., BSgenome.Hsapiens.UCSC.hg38).

Key Parameters

• geneModel (no default): A GRangesList object describing the gene structure.
• targetGene (no default): Character string specifying the name of the target gene.
• from (NULL): Numeric coordinate specifying the start of the plot window.
• to (NULL): Numeric coordinate specifying the end of the plot window.
• extend.left (0): Numeric value to extend the plot window to the left.
• extend.right (0): Numeric value to extend the plot window to the right.
• showGuideLabels (TRUE): Logical indicating whether to display gRNA labels.
• pamSiteOnly (FALSE): Logical indicating whether to plot only the PAM site instead of the full protospacer.
• onTargetScore (NULL): Character string specifying the metadata column name containing on-target scores.
• annotations (NULL): Named list of GRanges objects representing genomic annotations.
• gcWindow (NULL): Integer specifying the window size for calculating percent GC content.

Best Practices

• Window Adjustment: Adjust the plot window manually using from, to, extend.left, and extend.right to show the entire gene or focus on a specific exon.
• Crowding Prevention: Set showGuideLabels = FALSE when plotting a large number of candidate gRNAs to avoid crowding the plot space.
• PAM Site Only: Set pamSiteOnly = TRUE when visualizing many overlapping gRNAs in a small window to simplify the plot.
• Pre-filtering: Filter out gRNAs overlapping repeat elements or SNPs using crisprDesign::removeRepeats before plotting to ensure high-quality selections.

Common Pitfalls

• Rendering Errors: Plotting too many gene isoforms or gRNAs in a small graphical device, resulting in rendering errors. Fix: Increase the height/width of the plot space using grDevices::quartz or similar device settings.

Alternatives

• Gviz: For general genomic track visualization (which crisprViz is built upon).
• biovizBase: For nucleotide color schemes and basic genomic plotting utilities.

Citations

• No specific primary publication is cited in the vignette text, but the package is part of the crisprVerse ecosystem.

References

• Homepage: bioconductor.org/packages/crisprViz
• Vignette: bioconductor.org/packages/release/bioc/vignettes/crisprViz/inst/doc/introduction.html