## ----include=FALSE------------------------------------------------------------ knitr::opts_chunk$set(message=FALSE, warning=FALSE) ## ----eval=FALSE--------------------------------------------------------------- # install.packages("BiocManager") # BiocManager::install("crisprViz") ## ----message=FALSE, warning=FALSE--------------------------------------------- library(BSgenome.Hsapiens.UCSC.hg38) library(crisprDesign) library(crisprViz) ## ----------------------------------------------------------------------------- data("krasGuideSet", package="crisprViz") data("krasGeneModel", package="crisprViz") length(krasGuideSet) # number of candidate gRNAs ## ----------------------------------------------------------------------------- plotGuideSet(krasGuideSet[1:4], geneModel=krasGeneModel, targetGene="KRAS") ## ----------------------------------------------------------------------------- from <- min(start(krasGeneModel$transcripts)) to <- max(end(krasGeneModel$transcripts)) plotGuideSet(krasGuideSet[1:4], geneModel=krasGeneModel, targetGene="KRAS", from=from, to=to, extend.left=1000, extend.right=1000) ## ----fig.height=10------------------------------------------------------------ plotGuideSet(krasGuideSet, geneModel=krasGeneModel, targetGene="KRAS", showGuideLabels=FALSE, from=from, to=to, extend.left=1000, extend.right=1000) ## ----------------------------------------------------------------------------- # new window range around target exon targetExon <- queryTxObject(krasGeneModel, featureType="cds", queryColumn="exon_id", queryValue="ENSE00000936617") targetExon <- unique(targetExon) from <- start(targetExon) to <- end(targetExon) plotGuideSet(krasGuideSet, geneModel=krasGeneModel, targetGene="KRAS", from=from, to=to, extend.left=20, extend.right=20) ## ----------------------------------------------------------------------------- plotGuideSet(krasGuideSet, geneModel=krasGeneModel, targetGene="KRAS", from=from, to=to, extend.left=20, extend.right=20, pamSiteOnly=TRUE) ## ----message=FALSE, warning=FALSE--------------------------------------------- selectedGuides <- c("spacer_80", "spacer_84", "spacer_88", "spacer_92", "spacer_96", "spacer_100", "spacer_104", "spacer_108", "spacer_112") candidateGuides <- krasGuideSet[selectedGuides] plotGuideSet(candidateGuides, geneModel=krasGeneModel, targetGene="KRAS", onTargetScore="score_deephf") ## ----------------------------------------------------------------------------- data("gpr21GuideSet", package="crisprViz") data("gpr21GeneModel", package="crisprViz") ## ----fig.height=4, fig.width=6------------------------------------------------ plotGuideSet(gpr21GuideSet, geneModel=gpr21GeneModel, targetGene="GPR21", bsgenome=BSgenome.Hsapiens.UCSC.hg38, margin=0.3) ## ----fig.height=4, fig.width=10----------------------------------------------- # increase plot width from 6" to 10" plotGuideSet(gpr21GuideSet, geneModel=gpr21GeneModel, targetGene="GPR21", bsgenome=BSgenome.Hsapiens.UCSC.hg38, margin=0.3) ## ----------------------------------------------------------------------------- data("mmp7GuideSet", package="crisprViz") data("mmp7GeneModel", package="crisprViz") ## ----------------------------------------------------------------------------- data("repeats", package="crisprViz") ## ----------------------------------------------------------------------------- from <- min(start(mmp7GuideSet)) to <- max(end(mmp7GuideSet)) plotGuideSet(mmp7GuideSet, geneModel=mmp7GeneModel, targetGene="MMP7", guideStacking="dense", annotations=list(Repeats=repeats), pamSiteOnly=TRUE, from=from, to=to, extend.left=600, extend.right=100, includeSNPTrack=TRUE) ## ----------------------------------------------------------------------------- filteredGuideSet <- crisprDesign::removeRepeats(mmp7GuideSet, gr.repeats=repeats) filteredGuideSet <- filteredGuideSet[!filteredGuideSet$hasSNP] plotGuideSet(filteredGuideSet, geneModel=mmp7GeneModel, targetGene="MMP7", guideStacking="dense", annotations=list(Repeats=repeats), pamSiteOnly=TRUE, from=from, to=to, extend.left=600, extend.right=100, includeSNPTrack=TRUE) ## ----------------------------------------------------------------------------- data("cage", package="crisprViz") data("dnase", package="crisprViz") ## ----------------------------------------------------------------------------- plotGuideSet(filteredGuideSet, geneModel=mmp7GeneModel, targetGene="MMP7", guideStacking="dense", annotations=list(CAGE=cage, DNase=dnase), pamSiteOnly=TRUE, from=from, to=to, extend.left=600, extend.right=100) ## ----------------------------------------------------------------------------- # filter GuideSet for gRNAs overlapping DNase track overlaps <- findOverlaps(filteredGuideSet, dnase, ignore.strand=TRUE) finalGuideSet <- filteredGuideSet[queryHits(overlaps)] plotGuideSet(finalGuideSet, geneModel=mmp7GeneModel, targetGene="MMP7", guideStacking="dense", annotations=list(CAGE=cage, DNase=dnase), pamSiteOnly=TRUE, margin=0.4) ## ----------------------------------------------------------------------------- data("cas9GuideSet", package="crisprViz") data("cas12aGuideSet", package="crisprViz") data("ltn1GeneModel", package="crisprViz") ## ----fig.height=8------------------------------------------------------------- plotMultipleGuideSets(list(SpCas9=cas9GuideSet, AsCas12a=cas12aGuideSet), geneModel=ltn1GeneModel, targetGene="LTN1", bsgenome=BSgenome.Hsapiens.UCSC.hg38, margin=0.2, gcWindow=10) ## ----eval=FALSE--------------------------------------------------------------- # grDevices::quartz("Example plot", width=6, height=7) # # plot function ## ----------------------------------------------------------------------------- sessionInfo()