R/read_dist.R

In SchlossLab/schtools: Schloss Lab Tools for Reproducible Microbiome Research

#' Read in lower left triangular matrix from file
#'
#' @param dist_filename filename of lower left triangular matrix (.dist)
#'
#' @return distance matrix as a tibble
#' @export
#' @author Nick Lesniak, \email{nlesniak@@umich.edu}
#'
#' @examples
#' dist_filepath <- system.file("extdata",
#'   "sample.final.thetayc.0.03.lt.ave.dist",
#'   package = "schtools"
#' )
#' dist_tbl <- read_dist(dist_filepath)
#' head(dist_tbl)
read_dist <- function(dist_filename) {
  distances <- rows <- NULL
  # TODO: input validation - make sure file has expected format & throw errors if it doesn't
  # read in the first row to determine the matrix dimensions
  matrix_dim <-
    as.numeric(utils::read.table(dist_filename, nrows = 1, as.is = TRUE))
  # read in all the data from the lower triangle (exclude the first which is the matrix dim)
  distance_matrix <- utils::read.table(dist_filename,
    fill = TRUE,
    skip = 1,
    col.names = c(as.character(1:matrix_dim)),
    stringsAsFactors = F
  )
  # add column names based on row names
  colnames(distance_matrix) <- c("rows", distance_matrix$X1[-matrix_dim])
  # convert to long form and eliminate NAs (upper right of triangle)
  return(
    distance_matrix %>%
      tidyr::pivot_longer(
        cols = -rows,
        values_to = "distances",
        names_to = "columns"
      ) %>%
      dplyr::filter(!is.na(distances))
  )
}