## ---- include=FALSE----------------------------------------------------------- library(knitr) opts_chunk$set(concordance=FALSE) knitr::opts_chunk$set(fig.width = 18) knitr::opts_chunk$set(fig.height = 12) set.seed(21666641) ## ----getPackage, eval=FALSE--------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("CopyNumberPlots") ## ---- eval = FALSE------------------------------------------------------------ # BiocManager::install("bernatgel/CopyNumberPlots") ## ----------------------------------------------------------------------------- library(CopyNumberPlots) s1.file <- system.file("extdata", "S1.rawdata.txt", package = "CopyNumberPlots", mustWork = TRUE) s1 <- loadSNPData(s1.file) s1 ## ---- fig.wide=TRUE----------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") ## ---- fig.wide=TRUE----------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") plotBAF(kp, s1) ## ---- fig.wide=TRUE----------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") plotLRR(kp, s1) ## ---- fig.wide=TRUE----------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") plotBAF(kp, s1, r0=0.55, r1=1) plotLRR(kp, s1, r0=0, r1=0.45) ## ----------------------------------------------------------------------------- s1.calls.file <- system.file("extdata", "S1.segments.txt", package = "CopyNumberPlots", mustWork = TRUE) s1.calls <- loadCopyNumberCalls(s1.calls.file) s1.calls ## ---- fig.wide=TRUE----------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") plotBAF(kp, s1, r0=0.6, r1=1) plotLRR(kp, s1, r0=0.15, r1=0.55) #plotCopyNumberCalls(kp, s1.calls, r0=0, r1=0.10) ## ----------------------------------------------------------------------------- raw.data.file <- system.file("extdata", "snp.data_test.csv", package = "CopyNumberPlots", mustWork=TRUE) snps <- loadSNPData(raw.data.file) snps ## ----------------------------------------------------------------------------- cn.data <- toGRanges(c("chr14:66459785-86459774", "chr17:68663111-88866308", "chr10:43426998-83426994", "chr3:88892741-120892733", "chr2:12464318-52464316", "chrX:7665575-27665562")) cn.data$CopyNumberInteger <- sample(c(0,1,3,4), size = 6, replace = TRUE) cn.data$LossHetero <- cn.data$CopyNumberInteger<2 cn.data ## ----------------------------------------------------------------------------- cn.calls <- loadCopyNumberCalls(cn.data) cn.calls ## ----------------------------------------------------------------------------- kp <- plotKaryotype(plot.type = 1) #plotCopyNumberCalls(kp, cn.calls = cn.calls) ## ----------------------------------------------------------------------------- s1.file <- system.file("extdata", "S1.rawdata.txt", package = "CopyNumberPlots", mustWork = TRUE) s1 <- loadSNPData(s1.file) head(s1) s2.file <- system.file("extdata", "S2.rawdata.txt", package = "CopyNumberPlots", mustWork = TRUE) s2 <- loadSNPData(s2.file) head(s2) ## ----------------------------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") plotBAF(kp, snps=s1) ## ----------------------------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") plotBAF(kp, snps=s1, r0=0, r1=0.2, labels = "BAF1", points.col = "orange", points.cex = 2, points.pch = 4, axis.cex = 0.3) plotBAF(kp, snps=s1, r0=0.3, r1=0.5, labels = "BAF2", points.col = "red", points.cex = 0.5, points.pch = 8, axis.cex = 0.7) plotBAF(kp, snps=s1, r0=0.6, r1=1, labels = "BAF3", points.col = "#FF552222", points.cex = 1.8, points.pch = 16, axis.cex = 0.7) ## ----------------------------------------------------------------------------- samples <- list("Sample1"=s1, "Sample2"=s2) kp <- plotKaryotype(chromosomes="chr1") plotBAF(kp, snps=samples) ## ----------------------------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") kpAddBaseNumbers(kp) plotLRR(kp, snps=s1) ## ----------------------------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") kpAddBaseNumbers(kp) plotLRR(kp, snps=s1, ymin=-1.5, ymax=1.5) ## ----------------------------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") kpAddBaseNumbers(kp) plotLRR(kp, snps=s1, ymin=-1.5, ymax=1.5, out.of.range = "density") ## ----------------------------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") plotLRR(kp, snps=s1, ymin=-1.5, ymax=1.5, out.of.range = "density", density.window = 1e6) ## ----------------------------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") plotLRR(kp, snps=s1, r0=0, r1=0.2, labels = "LRR1", points.col = "orange", points.cex = 2, points.pch = 4, axis.cex = 0.3) plotLRR(kp, snps=s1, r0=0.3, r1=0.5, labels = "LRR2", points.col = "red", points.cex = 0.5, points.pch = 8, axis.cex = 0.7, ymin=-1.5, ymax=1.5, out.of.range.col = "gold", out.of.range = "density", density.window = 10e6, density.height = 0.3) plotLRR(kp, snps=s1, r0=0.6, r1=1, labels = "LRR3", points.col = "#FF552222", points.cex = 1.8, points.pch = 16, axis.cex = 0.7) ## ----------------------------------------------------------------------------- s1.calls.file <- system.file("extdata", "S1.segments.txt", package = "CopyNumberPlots", mustWork = TRUE) s1.calls <- loadCopyNumberCalls(s1.calls.file) s2.calls <- loadCopyNumberCalls(system.file("extdata", "S2.segments.txt", package = "CopyNumberPlots", mustWork = TRUE)) s3.calls <- loadCopyNumberCalls(system.file("extdata", "S3.segments.txt", package = "CopyNumberPlots", mustWork = TRUE)) s1.calls ## ---- fig.wide=TRUE----------------------------------------------------------- kp <- plotKaryotype(chromosomes = "chr1") #plotCopyNumberCalls(kp, s1.calls) ## ---- fig.wide=TRUE----------------------------------------------------------- kp <- plotKaryotype(chromosomes="chr1") #plotCopyNumberCalls(kp, s1.calls, cn.colors = "red_blue", loh.color = "orange", r1=0.8) cn.cols <- getCopyNumberColors(colors = "red_blue") legend("top", legend=names(cn.cols), fill = cn.cols, ncol=length(cn.cols)) ## ---- fig.wide=TRUE----------------------------------------------------------- cn.calls <- list("Sample1"=s1.calls, "Sample2"=s2.calls, "Sample3"=s3.calls) kp <- plotKaryotype(chromosomes="chr1") #plotCopyNumberCalls(kp, cn.calls, r1=0.3) ## ---- fig.wide=TRUE----------------------------------------------------------- kp <- plotKaryotype(chr="chr1") #plotCopyNumberCallsAsLines(kp, s1.calls) ## ---- fig.wide=TRUE----------------------------------------------------------- kp <- plotKaryotype(chr="chr1") #plotCopyNumberCallsAsLines(kp, s1.calls, style = "segments") ## ----------------------------------------------------------------------------- cn.cols <- getCopyNumberColors(colors = "green_orange_red") kp <- plotKaryotype(chromosomes="chr1") kpDataBackground(kp, color = cn.cols["2"], r0=0.3) #plotCopyNumberCalls(kp, cn.calls, loh.height = 0, r0=0.3) #plotCopyNumberSummary(kp, cn.calls, r1=0.25) ## ----------------------------------------------------------------------------- cn.cols <- getCopyNumberColors(colors = "green_orange_red") kp <- plotKaryotype(chromosomes="chr1") kpDataBackground(kp, color = cn.cols["2"], r0=0.3) #plotCopyNumberCalls(kp, cn.calls, loh.height = 0, r0=0.3) #plotCopyNumberSummary(kp, cn.calls, r1=0.25, direction = "out") ## ----------------------------------------------------------------------------- sessionInfo()