## ---- include=FALSE------------------------------------------------------ #This block gets rid of the import messages library("wiggleplotr") library("GenomicRanges") library("dplyr") library("biomaRt") library("GenomicFeatures") library("ensembldb") library("EnsDb.Hsapiens.v86") library("org.Hs.eg.db") library("TxDb.Hsapiens.UCSC.hg38.knownGene") ## ---- eval = FALSE------------------------------------------------------- # source("http://www.bioconductor.org/biocLite.R") # biocLite("wiggleplotr") ## ------------------------------------------------------------------------ library("wiggleplotr") library("dplyr") library("GenomicRanges") library("GenomicFeatures") library("biomaRt") ## ------------------------------------------------------------------------ ncoa7_metadata names(ncoa7_exons) names(ncoa7_cdss) ## ------------------------------------------------------------------------ plotTranscripts(ncoa7_exons, ncoa7_cdss, ncoa7_metadata, rescale_introns = FALSE) ## ------------------------------------------------------------------------ plotTranscripts(ncoa7_exons, ncoa7_cdss, ncoa7_metadata, rescale_introns = TRUE) ## ------------------------------------------------------------------------ plotTranscripts(ncoa7_exons, rescale_introns = TRUE) ## ------------------------------------------------------------------------ sample_data = dplyr::data_frame( sample_id = c("aipt_A", "aipt_C", "bima_A", "bima_C"), condition = factor(c("Naive", "LPS", "Naive", "LPS"), levels = c("Naive", "LPS")), scaling_factor = 1) sample_data = sample_data %>% dplyr::mutate(bigWig = system.file("extdata", paste0(sample_id, ".str2.bw"), package = "wiggleplotr")) as.data.frame(sample_data) ## ------------------------------------------------------------------------ track_data = dplyr::mutate(sample_data, track_id = condition, colour_group = condition) ## ------------------------------------------------------------------------ selected_transcripts = c("ENST00000438495", "ENST00000392477") #Plot only two transcripts of the gens plotCoverage(ncoa7_exons[selected_transcripts], ncoa7_cdss[selected_transcripts], ncoa7_metadata, track_data, heights = c(2,1), fill_palette = getGenotypePalette()) ## ------------------------------------------------------------------------ plotCoverage(ncoa7_exons[selected_transcripts], ncoa7_cdss[selected_transcripts], ncoa7_metadata, track_data, heights = c(2,1), fill_palette = getGenotypePalette(), mean_only = FALSE, alpha = 0.5) ## ------------------------------------------------------------------------ track_data = dplyr::mutate(sample_data, track_id = "RNA-seq", colour_group = condition) plotCoverage(ncoa7_exons[selected_transcripts], ncoa7_cdss[selected_transcripts], ncoa7_metadata, track_data, heights = c(2,1), fill_palette = getGenotypePalette(), coverage_type = "line") ## ---- eval = FALSE------------------------------------------------------- # track_data = dplyr::mutate(sample_data, track_id = "RNA-seq", colour_group = condition) # plotCoverage(ncoa7_exons[selected_transcripts], ncoa7_cdss[selected_transcripts], # ncoa7_metadata, track_data, # heights = c(2,1), fill_palette = getGenotypePalette(), coverage_type = "line", # connect_exons = FALSE, transcript_label = FALSE, rescale_introns = FALSE) ## ------------------------------------------------------------------------ library("ensembldb") library("EnsDb.Hsapiens.v86") plotTranscriptsFromEnsembldb(EnsDb.Hsapiens.v86, gene_names = "NCOA7", transcript_ids = c("ENST00000438495", "ENST00000392477")) ## ------------------------------------------------------------------------ #Load OrgDb and TxDb objects with UCSC gene annotations require("org.Hs.eg.db") require("TxDb.Hsapiens.UCSC.hg38.knownGene") plotTranscriptsFromUCSC(orgdb = org.Hs.eg.db, txdb = TxDb.Hsapiens.UCSC.hg38.knownGene, gene_names = "NCOA7", transcript_ids = c("uc003qae.5", "uc063rdt.2")) ## ------------------------------------------------------------------------ ensembl_mart = useMart("ENSEMBL_MART_ENSEMBL", host = "dec2014.archive.ensembl.org") ensembl_dataset = useDataset("hsapiens_gene_ensembl",mart=ensembl_mart) ensembl_dataset ## ------------------------------------------------------------------------ attributes = listAttributes(ensembl_dataset) head(attributes) ## ------------------------------------------------------------------------ selected_attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name", "strand", "gene_biotype", "transcript_biotype") data = getBM(attributes = selected_attributes, mart = ensembl_dataset) head(data) ## ------------------------------------------------------------------------ data = dplyr::rename(data, transcript_id = ensembl_transcript_id, gene_id = ensembl_gene_id, gene_name = external_gene_name) head(data) ## ------------------------------------------------------------------------ temporary_file = tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".rds") saveRDS(data, temporary_file) ## ------------------------------------------------------------------------ transcript_metadata = readRDS(temporary_file) head(transcript_metadata) ## ----eval=FALSE---------------------------------------------------------- # txdb = makeTxDbFromBiomart(biomart = "ENSEMBL_MART_ENSEMBL", # dataset = "hsapiens_gene_ensembl", # host="dec2014.archive.ensembl.org") ## ----eval=FALSE---------------------------------------------------------- # txdb_file = tempfile(pattern = "file", tmpdir = tempdir(), fileext = ".rds") # saveDb(txdb, txdb_file) ## ---- eval=FALSE--------------------------------------------------------- # txdb = loadDb(txdb_file) ## ---- eval=FALSE--------------------------------------------------------- # exons = exonsBy(txdb, by = "tx", use.names = TRUE) # cdss = cdsBy(txdb, by = "tx", use.names = TRUE) ## ---- eval=FALSE--------------------------------------------------------- # selected_transcripts = transcript_metadata %>% # dplyr::filter(gene_name == "NCOA7", transcript_biotype == "protein_coding") # tx_ids = selected_transcripts$transcript_id # plotTranscripts(exons[tx_ids], cdss[tx_ids], # transcript_metadata, rescale_introns = TRUE)