R/TutorialManifest.R

In sagrudd/cDNA_tutorial: Tutorial For Nanopore Sequence Based Gene Expression Profiling

knownTutorials <- c("cDNADiffExpr", "SeqStatsQC")

#' Prepare a volcanoPlot of gene expression data using ggplot2
#'
#' Volcano plot presents a scatter plot of the -log10(p-value) / log2 gene
#' expression from a differential gene expression study
#'
#' @param tutorialId name describing tutorial to initialise
#'
#' @return None
#'
#' @author Oxford Nanopore Bioinformatics, \email{support@@nanoporetech.com}
#' @references \url{https://en.wikipedia.org/wiki/Volcano_plot_(statistics)}
#' @keywords volcano
#'
#' @export
InitTutorial <- function(tutorialId) {
  if (tutorialId %in% knownTutorials) {
    if (tutorialId == "cDNADiffExpr") initcDNA()
    if (tutorialId == "SeqStatsQC")   initSeqStats()
  } else {
    stop(paste("[",tutorialId,"] is not a known tutorial"))
  }
}


initcDNA <- function() {
  
  # RawSequences
  
  cdna_seq_files <- c("condition1_rep1.fastq.gz", "condition1_rep2.fastq.gz", "condition1_rep3.fastq.gz", 
    "condition2_rep1.fastq.gz", "condition2_rep2.fastq.gz", "condition2_rep3.fastq.gz")
  migrate(file.path("extdata", "cdna_differential_expression", cdna_seq_files), "RawData")
  
  # RMD template, config file and Snakefile
  cdna_workflow_files <- c("Nanopore_cDNA_Tutorial.Rmd", "config.yaml", "Snakefile")
  migrate(file.path("extdata", "cdna_differential_expression", cdna_workflow_files), ".")
  
  # graphics and accompanying images
  image_files <- c("dag1.png", "ExperimentalDesign.png", "FolderLayout.png", "KnitIt.png")
  migrate(file.path("extdata", "cdna_differential_expression", image_files), file.path("Analysis", "StaticImages"))
}


initSeqStats <- function() {
  # Raw sequence summary file
  migrate(file.path("extdata", "sequencing_statistics_qc", "merged_seq_summary.txt.bz2"), "RawData")
  # RMD template, config file and Snakefile
  seqstat_workflow_files <- c("Nanopore_SumStatQC_Tutorial.Rmd", "config.yaml")
  migrate(file.path("extdata", "sequencing_statistics_qc", seqstat_workflow_files), ".")
  # graphics and accompanying images
  image_files <- c("sumstatEditParams.png", "KnitIt.png")
  migrate(file.path("extdata", "sequencing_statistics_qc", image_files), file.path("Analysis", "StaticImages"))
}



migrate <- function(source, destination) {
  dir.create(destination, showWarnings=FALSE, recursive = TRUE)
  file.copy(system.file(source, package="TuPoreIal"), destination)
}