## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- # loading the rGenomeTracks library(rGenomeTracks) # loading example data #library(rGenomeTracksData) ## ----eval=FALSE--------------------------------------------------------------- # install_pyGenomeTracks() ## ----eval=FALSE--------------------------------------------------------------- # # Download h5 example # ah <- AnnotationHub() # query(ah, "rGenomeTracksData") # h5_dir <- ah[["AH95901"]] # # # Create HiC track from HiC matrix # h5 <- track_hic_matrix( # file = h5_dir, depth = 250000, min_value = 5, max_value = 200, # transform = "log1p", show_masked_bins = FALSE # ) # ## ----------------------------------------------------------------------------- # Load other examples tads_dir <- system.file("extdata", "tad_classification.bed", package = "rGenomeTracks") arcs_dir <- system.file("extdata", "links2.links", package = "rGenomeTracks") bw_dir <- system.file("extdata", "bigwig2_X_2.5e6_3.5e6.bw", package = "rGenomeTracks") # Create TADS track tads <- track_domains( file = tads_dir, border_color = "black", color = "none", height = 5, line_width = 5, show_data_range = FALSE, overlay_previous = "share-y" ) # Create arcs track arcs <- track_links( file = arcs_dir, links_type = "triangles", line_style = "dashed", overlay_previous = "share-y", color = "darkred", line_width = 3, show_data_range = FALSE ) # Create bigwig track bw <- track_bigwig( file = bw_dir, color = "red", max_value = 50, min_value = 0, height = 4, overlay_previous = "no", show_data_range = FALSE ) ## ----------------------------------------------------------------------------- # Create one object from HiC, arcs and bigwid tracks <- tads + arcs + bw ## ----eval=FALSE--------------------------------------------------------------- # # Plot the tracks # ## Note to verify installing miniconda if not installed. # # layout(matrix(c(1,1,2,3,4,4), nrow = 3, ncol = 2, byrow = TRUE)) # plot_gtracks(tracks, chr = "X", start = 25 * 10^5, end = 31 * 10^5) # # # Plot HiC, TADS and bigwig tracks # plot_gtracks(h5 + tads + bw, chr = "X", start = 25 * 10^5, end = 31 * 10^5) ## ----echo=FALSE--------------------------------------------------------------- plot(imager::load.image(system.file("extdata", "images/example1.png", package = "rGenomeTracks")), axes = FALSE) plot(imager::load.image(system.file("extdata", "images/example2.png", package = "rGenomeTracks")), axes = FALSE) ## ----------------------------------------------------------------------------- dirs <- list.files(system.file("extdata", package = "rGenomeTracks"), full.names = TRUE) # filter only bed files (without bedgraphs or narrowpeaks) bed_dirs <- grep( dirs, pattern = ".bed(?!graph)", perl = TRUE, value = TRUE) bed_list <- lapply(bed_dirs, track_bed) bed_tracks <- Reduce("+", bed_list) ## ----------------------------------------------------------------------------- sessionInfo()