## ---- 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------------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly=TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("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("ENST00000438495.6", "ENST00000368357.7"))

## -----------------------------------------------------------------------------
ensembl_mart = useMart("ENSEMBL_MART_ENSEMBL", host = "jan2020.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="jan2020.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)