## ----eval = TRUE, echo=FALSE, results="hide", warning=FALSE------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) suppressPackageStartupMessages({ library(GenomicRanges) library(ggplot2) library(magrittr) library(VplotR) }) ## ----eval = FALSE------------------------------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("VplotR") # library("VplotR") ## ----eval = TRUE-------------------------------------------------------------- library(VplotR) bamfile <- system.file("extdata", "ex1.bam", package = "Rsamtools") fragments <- importPEBamFiles( bamfile, shift_ATAC_fragments = TRUE ) fragments ## ----eval = TRUE-------------------------------------------------------------- data(ce11_proms) ce11_proms data(ATAC_ce11_Serizay2020) ATAC_ce11_Serizay2020 ## ----eval = TRUE-------------------------------------------------------------- data(ABF1_sacCer3) ABF1_sacCer3 data(MNase_sacCer3_Henikoff2011) MNase_sacCer3_Henikoff2011 ## ----eval = TRUE-------------------------------------------------------------- df <- getFragmentsDistribution( MNase_sacCer3_Henikoff2011, ABF1_sacCer3 ) p <- ggplot(df, aes(x = x, y = y)) + geom_line() + theme_ggplot2() p ## ----eval = TRUE-------------------------------------------------------------- p <- plotVmat(x = MNase_sacCer3_Henikoff2011, granges = ABF1_sacCer3) p ## ----eval = TRUE-------------------------------------------------------------- list_params <- list( "MNase\n@ ABF1" = list(MNase_sacCer3_Henikoff2011, ABF1_sacCer3), "MNase\n@ random loci" = list( MNase_sacCer3_Henikoff2011, sampleGRanges(ABF1_sacCer3) ) ) p <- plotVmat( list_params, cores = 1 ) p ## ----eval = TRUE-------------------------------------------------------------- list_params <- list( "Germline ATACseq\n@ Ubiq. proms" = list( ATAC_ce11_Serizay2020[['Germline']], ce11_proms[ce11_proms$which.tissues == 'Ubiq.'] ), "Germline ATACseq\n@ Germline proms" = list( ATAC_ce11_Serizay2020[['Germline']], ce11_proms[ce11_proms$which.tissues == 'Germline'] ), "Neuron ATACseq\n@ Ubiq. proms" = list( ATAC_ce11_Serizay2020[['Neurons']], ce11_proms[ce11_proms$which.tissues == 'Ubiq.'] ), "Neuron ATACseq\n@ Neuron proms" = list( ATAC_ce11_Serizay2020[['Neurons']], ce11_proms[ce11_proms$which.tissues == 'Neurons'] ) ) p <- plotVmat( list_params, cores = 1, nrow = 2, ncol = 5 ) p ## ----eval = TRUE-------------------------------------------------------------- # No normalization p <- plotVmat( list_params, cores = 1, nrow = 2, ncol = 5, verbose = FALSE, normFun = 'none' ) p ## ----eval = TRUE-------------------------------------------------------------- # Library depth + number of loci of interest (default) p <- plotVmat( list_params, cores = 1, nrow = 2, ncol = 5, verbose = FALSE, normFun = 'libdepth+nloci' ) p ## ----eval = TRUE-------------------------------------------------------------- # Zscore p <- plotVmat( list_params, cores = 1, nrow = 2, ncol = 5, verbose = FALSE, normFun = 'zscore' ) p # Quantile p <- plotVmat( list_params, cores = 1, nrow = 2, ncol = 5, verbose = FALSE, normFun = 'quantile', s = 0.99 ) p ## ----------------------------------------------------------------------------- p <- plotFootprint( MNase_sacCer3_Henikoff2011, ABF1_sacCer3 ) p ## ----------------------------------------------------------------------------- data(MNase_sacCer3_Henikoff2011_subset) genes_sacCer3 <- GenomicFeatures::genes(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene:: TxDb.Scerevisiae.UCSC.sacCer3.sgdGene ) p <- plotProfile( fragments = MNase_sacCer3_Henikoff2011_subset, window = "chrXV:186,400-187,400", loci = ABF1_sacCer3, annots = genes_sacCer3, min = 20, max = 200, alpha = 0.1, size = 1.5 ) p ## ----echo = TRUE, collapse = TRUE, eval = TRUE-------------------------------- sessionInfo()