R/getFilename.r

In igordot/copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

####################################################################
## Author: Gro Nilsen, Knut Liestøl and Ole Christian Lingjærde.
## Maintainer: Gro Nilsen <gronilse@ifi.uio.no>
## License: Artistic 2.0
## Part of the copynumber package
## Reference: Nilsen and Liestøl et al. (2012), BMC Genomics
####################################################################

# Function that checks and returns valid filename(s):

## Input:
### nPage: number of plot pages
### file.name: input desired file.name
### ID: a vector of IDs for each plot page; eg chromosome number or sample name
### type: plot type

## Output:
### file.name: a vector giving valid filename(s)

## Required by:
### plotAllele
### plotChrom
### plotGenome
### plotSample




## Requires:
### none

getFilename <- function(nPage, file.name, ID, type) {
  def.name <- switch(type,
    genome = "genomeplot",
    sample = "sampleplot",
    chromosome = "chromosomeplot",
    aspcf = "aspcfplot",
    genomeFreq = "genome frequencyplot",
    chromFreq = "chromosome frequencyplot",
    genomeHeat = "genome heatplot",
    chromHeat = "chromosome heatplot"
  )
  if (nPage == 1) {
    # Only one file/window
    if (is.null(file.name)) {
      file.name <- ifelse(length(ID) == 1, paste(def.name, "_", ID, sep = ""), def.name)
    } else {
      if (length(file.name) != nPage) {
        warning("Length of 'file.name' is not equal to number of files to be saved, first element in 'file.name' is used", call. = FALSE, immediate. = TRUE)
      }
      file.name <- file.name[1] # in case more than one name has been specified
    }
  } else {
    # Each page should be in separate file/window, need multiple file.names
    if (is.null(file.name)) {
      file.name <- paste(def.name, "_", ID, sep = "")
      # Check that number of file names matches number of pages; if not set file.name to genomeplot 1, .., nPage
      if (length(file.name) != nPage) {
        file.name <- paste(def.name, 1:nPage, sep = "")
      }
    } else {
      if (length(file.name) < nPage) {
        file.name <- paste(file.name[1], 1:nPage, sep = "")
        warning("Length of 'file.name' is less than number of files to be saved, first element in 'file.name' is reused", call. = FALSE, immediate. = TRUE)
      } else {
        if (length(file.name) > nPage) {
          file.name <- file.name[1:nPage]
        }
      }
    } # endif
  } # endif

  return(file.name)
} # endfunction