R/utils.R

In InouyeLab/NetRep: Permutation Testing Network Module Preservation Across Datasets

### Value Matching and Subsetting
### 
### @description
### This set of functions provides shortcuts for value matching and subsetting,
### on top of the functionality provided by \code{\link[base]{\%in\%}}.
### 
### \code{\%nin\%} returns a logical vector indicating if elements of \code{x} 
### are not in \code{table}, This is the opposite of \code{\%in\%}.
### 
### \code{\%sub_in\%} returns the elements \code{x} that are \code{\%in\%} 
### \code{table} rather than a logical vector.
### 
### \code{\%sub_nin\%} returns the elements \code{x} that are \code{\%nin\%} 
### \code{table} rather than a logical vector.
### 
### @param x vector or \code{NULL}: the values to be matched. \link[base]{Long vectors} 
###   are supported.
### @param table vector or \code{NULL}: the values to be matched against. 
###   \link[base]{Long vectors} are not supported.
### @name matchsub
NULL

### @rdname matchsub
### @keywords internal
`%nin%` <- function(x, table) !(x %in% table)

### @rdname matchsub
### @keywords internal
`%sub_in%` <- function(x, table) x[x %in% table]

### @rdname matchsub
### @keywords internal
`%sub_nin%` <- function(x, table) x[x %nin% table]

### Verbose Concatenate and Print with Indentation
### 
### Concatenate and output the objects only if the \code{verbose} flag is set 
### to \code{TRUE}. Allows for indentation, adding a series of spaces to the 
### beginning of each line, 2 for every increment in \code{ind}. 
### 
### @details
###  \code{vCat} is slightly more intelligent than regulat \code{cat} in the way 
###  it formats the output and breaks it into lines. As a result, \code{fill} is 
###  set to \code{TRUE} by default. Another notable difference from \code{cat} is
###  the way newline objects are handled. For example, the call: 
###  \code{cat("hello", "world", "\\n", "foo", "bar")} won't wrap the newline 
###  character with spaces. This avoids the need to set \code{sep} to \code{""} 
###  and embed multiple \code{paste} calls. Finally, a newline character is 
###  appended to the end of the whole message, avoiding the need to manually 
###  specify this when calling \code{vCat}.
###  
### @seealso \code{\link[base]{cat}}
### @param verbose logical. If \code{TRUE}, passes the rest of the arguments to
###   \code{\link{cat}}
### @param ind an integer corresponding to the level of indentation. Each
###   indentation level corresponds to two spaces.
### @param ... Arguments to pass to \code{\link[base]{cat}}
### @param sep a character vector of strings to append after each element.
### @param fill a logical or (positive) numeric controlling how the output is 
###   broken into successive lines. If \code{FALSE}, only newlines created 
###   explicitly by "\\n" are printed. Otherwise, the output is broken into lines
###   with print width equal to the option width if fill is \code{TRUE} 
###   (default), or the value of fill if this is numeric. Non-positive fill 
###   values are ignored, with a warning.
### @param labels character vector of labels for the lines printed. Ignored if 
###   fill is \code{FALSE}.
###
### @keywords internal
vCat <- function(verbose, ind=0,  ..., sep=" ", fill=TRUE, labels=NULL) {
  if (!(is.vector(verbose) && !is.list(verbose) && is.logical(verbose) &&
        length(verbose) == 1 && !is.na(verbose))) {
    stop("'verbose' must be one of 'TRUE' or 'FALSE'")
  }
  
  if(verbose) {
    # Put a timestamp at the start of the message:
    if (is.null(labels))
      labels <- paste0("[", format(Sys.time(), usetz=TRUE), "] ")
    
    # We need to format each line with the indendation level
    if (ind > 0) {
      indent <- paste(rep("  ", ind), collapse="")
    } else {
      indent = ""
    }
    
    args <- list(...)
    if (is.null(names(args))) {
      str <- paste(args, collapse=sep)
      named <- NULL
    } else {
      str <- paste(args[names(args) == ""], collapse=sep)
      named <- args[names(args) != ""]
    }
    str <- gsub(" \n ", "\n", str) # make it easier to insert newlines
    lines <- strsplit(str, "\n")[[1]]
    # Handle automatic line wrapping
    if (fill) {
      if (is.logical(fill)) {
        fillWidth <- options("width")
      } else if (!is.numeric(fill)) {
        stop("invalid 'fill' argument")
      } else if (fill < 1) {
        warning("non-positive 'fill' argument will be ignored")
        fillWidth <- options("width")
      } else {
        fillWidth <- fill
      }
      words <- strsplit(lines, " ")
      # Create new lines by accumulating words in each line until the addition
      # of the next word would exceed the fillWidth. 
      formatted <- lapply(words, function(lw) {
        newlines <- c("")
        curnl <- 1
        for (w in lw) {
          if (newlines[curnl] == "") {
            newlines[curnl] <- paste0(labels, indent, w)
          } else if(nchar(newlines[curnl]) + 1 + nchar(w) < fillWidth) {
            newlines[curnl] <- paste(newlines[curnl], w)
          } else {
            curnl <- curnl + 1
            labels <- paste(rep(" ", nchar(labels)), collapse="")
            newlines[curnl] <- paste0(labels, indent, w)
          }
        }
        paste(newlines, collapse="\n")
      })
      lines <- strsplit(paste(formatted, collapse="\n"), "\n")[[1]]
    }
    str <- paste0(lines, "\n", collapse="")
    if (is.null(named)) {
      cat(str)
    } else {
      # build expression from remaining named arguments
      args = sapply(seq_along(named), function(n) {
        if (is.character(named[[n]])) {
          paste0(names(named)[n], "=", "'", named[[n]], "'")
        } else {
          paste0(names(named)[n], "=", named[[n]])
        }
      })
      eval(parse(text=paste0(paste0(c("cat(str", args), collapse=", "), ")")))
    }
  }
}

### Insert NAs into a vector at specified positions
### 
### Useful for inserting NAs into the correct positions when examining module 
### probes that do not exist in the test dataset.
### 
### @param vec vector to insert NAs to.
### @param na.indices indices the NAs should be located at in the final vector.
### 
### @return
### The vector with NAs inserted in the correct positions.
### 
### @keywords internal
insert.nas <- function(vec, na.indices) {
  res <- vector(typeof(vec), length(vec) + length(na.indices))
  res[na.indices] <- NA
  res[!is.na(res)] <- vec
  res
}

### Order the module vector numerically
### 
### The module assingments may be numeric, but coded as characters.
### 
### @param vec module vector to order
### 
### @return the order of the vector
### 
### @keywords internal
orderAsNumeric <- function(vec) {
  tryCatch({
    order(as.integer(vec))
  }, warning=function(w) {
    order(vec)
  })
}

### Remove unnecessary list structure 
###
### Removes entries that are \code{NULL} are extracts element if the length is 1.
###
### @param l a nested list
### @param depth depth to traverse to
### 
### @return a list
### 
### @keywords internal
simplifyList <- function(l, depth) {
  # Recursively traverse until we hit the depth requested or we cant go deeper
  stopifnot(is.numeric(depth) && depth > 0)
  if (depth == 1) {
    if (is.null(l)) {
      return(NULL)
    }
    # Delete empty leaf nodes
    for (ii in rev(seq_along(l))) {
      if (is.null(l[[ii]]))
        l[[ii]] <- NULL
    }
    if (length(l) == 0) {
      return(NULL)
    } else if (length(l) == 1) {
      return(l[[1]])
    } else {
      return(l) 
    }
  } else {
    for (ii in rev(seq_along(l))) {
      l[[ii]] <- simplifyList(l[[ii]], depth-1)
    }
    if (length(l) == 0) {
      return(NULL)
    } else if (length(l) == 1) {
      return(l[[1]])
    } else {
      return(l) 
    }
  }
}

### Get a sorted list of module names
### 
### If module labels are numeric, sorts numerically, otherwise sorts 
### alphabetically.
### 
### @param modules a vector of module labels to sort
### @return a sorted vector   
### 
### @keywords internal
sortModuleNames <- function(modules) {
  tryCatch({
    modules[order(as.numeric(modules))]
  }, warning=function(w) {
    sort(modules)
  })
}

### Load a \code{'disk.matrix'} into RAM
### 
### If \code{x} is a \code{\link{disk.matrix}} load in the matrix data at its
### associated file. If \code{x} is already a matrix, return as is.
### 
### @param x a \code{'matrix'} or \code{'disk.matrix'}
### 
### @return a \code{'matrix'}
### 
### @keywords internal
loadIntoRAM <- function(x) {
  if (is.null(x))
    return(NULL)
  as.matrix(x)
}

### Check if any objects are a 'disk.matrix'
### 
### @param ... objects to check.
### 
### @return 
###  \code{TRUE} if the class of any object in the list of input 
###  arguments is a "disk.matrix".
###  
### @keywords internal
any.disk.matrix <- function(...) {
  any(unlist(sapply(list(...), is.disk.matrix)))
}

### Silently check and load a package into the namespace
### 
### @param pkg name of the package to check
### 
### @return logical; \code{TRUE} if the package is installed and can be loaded.
### 
### @keywords internal
pkgReqCheck <- function(pkg) {
  suppressMessages(suppressWarnings(requireNamespace(pkg, quietly=TRUE)))
}

### Convert an absolute file path to a relative one if possible
### 
### @param file file path to convert
### 
### @return
###  a file path relative to either the users home directory or the current 
###  working directory if the file is located underneath either.
###  
### @keywords internal
prettyPath <- function(file) {
  file <- gsub("//", "/", file)
  file <- gsub(paste0(getwd(), "/?"), "", file)
  file <- gsub(normalizePath("~"), "~", file)
  file
}