R/helper_functions.R

In seqplots: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

#' Import function for narrowPeak format
#'
#' @param x the path or connection to .narrowPeak file
#'
#' @return GenomicRanges
#' @export 
#'
import.narrowPeak <- function(x) {
    extraCols <- c(signalValue="numeric", pValue="numeric", qValue="numeric",
                   peak="integer")
    gr <- import(x, format="bed", extraCols=extraCols)
    return(gr)
}



#' Converts numeric values labels with metric system suffix, i.e k, M, G, etc. 
#'
#' @param n The numeric value, that will be converted to label.
#' 
#' @return \code{character}
#'
#' @keywords internal
#' 
num2sci <- function( n ) {
    number <- abs(n)
    if(number == n) sign <- '' else sign <- '-'
    
    lut <- c(1e-24, 1e-21, 1e-18, 1e-15, 1e-12, 1e-09, 1e-06, 
             0.001, 1, 1000, 1e+06, 1e+09, 1e+12, 1e+15, 1e+18, 1e+21, 
             1e+24)
    pre <- c("y", "z", "a", "f", "p", "n", "u", "m", "", "k", 
             "M", "G", "T", "P", "E", "Z", "Y")
    ix <- findInterval(number, lut)
    if (lut[ix]!=1) {
        sistring <- paste0(
            sign, format(round(number/lut[ix], 3), digits = 3), pre[ix]
        )
        
    } else {
        sistring <- format(n, digits=3)
    }
    return(sistring)
}

#' Converts numeric values to labels with base pairs units, 
#' i.e bp, kb, Mb, Gb, etc. 
#'
#' @param n The numeric value, that will be converted to label.
#' 
#' @return \code{character}
#'
#' @keywords internal
#' 
num2bp <- function( n ) {
    if(n == 0)  return(paste0(0, 'bp'))
    
    number <- abs(n)
    if(number == n) sign <- '' else sign <- '-'
    
    lut <- c(1e-24, 1e-21, 1e-18, 1e-15, 1e-12, 1e-09, 1e-06, 
             0.001, 1, 1000, 1e+06, 1e+09, 1e+12, 1e+15, 1e+18, 1e+21, 
             1e+24)
    pre <- c("yb", "zb", "ab", "fb", "pb", "nb", "ub", "mb", "", "kb", 
             "Mb", "Gb", "Tb", "Pb", "Eb", "Zb", "Yb")
    ix <- findInterval(number, lut)
    if (lut[ix]!=1) {
        sistring <- paste0(
            sign, format(round(number/lut[ix], 3), digits = 3), pre[ix]
        )

    } else {
        sistring <- paste0(format(n, digits=3), 'bp')
    }
    return(sistring)
}

#' Get reference genome
#'
#' @param genome The filename of FASTA file or genome code for BSgenome
#' 
#' @return \code{DNAStringSet}
#'
#' @export
#' 
getREF <- function(genome) {
    
    if( file.exists(file.path(Sys.getenv('root'), 'genomes', genome)) ) {
        REF <- Biostrings::readDNAStringSet( file.path(Sys.getenv('root'), 'genomes', genome) )
        names(REF) <- gsub(' .+', '', names(REF))
    } else {
        
        GENOMES <- BSgenome::installed.genomes(
            splitNameParts=TRUE)$provider_version
        if( length(GENOMES) ) 
            names(GENOMES) <- gsub('^BSgenome.', '', BSgenome::installed.genomes())
        if( !length(GENOMES) ) stop('No genomes installed!')
        
        pkg <- paste0('BSgenome.', names(GENOMES[GENOMES %in% genome]))[[1]]
        suppressPackageStartupMessages(
            library(pkg, character.only = TRUE, quietly=TRUE)
        )
        REF <- get(pkg)
    }
    return(REF)
}