R/helper-functions.R

In phac-nml/pavian: Visualize and analyze metagenomics classification results

info_message <- function(...) {
  message("INFO [",format(Sys.time(), "%m/%d %H:%M"),"]: ",...)
}

startsWith <- function(x, prefix) {
  if (exists("startsWith", "package:base") ) {
    base::startsWith(x, prefix)
  } else {
    substring(x, 1, nchar(prefix)) == prefix
  }
}

get_col <- function(df, col) {
  if (!col %in% colnames(df)) {
    stop(col, " is not a column of df! Valid columns: ", paste(colnames(df), collapse=", "))
  }
  df[[col]]
}

rbind_w_common_columns <- function(...) {
  dat <- list(...)
  common_colnames <- Reduce(intersect, sapply(dat, colnames))
  Reduce(function(x,y) rbind(x[,common_colnames],y[,common_colnames]), dat)
}

common_buttons <- function(...) {
  opts <- list(...)
  dl_fname <- paste(unlist(c(opts, format(Sys.time(), "%y%m%d"))), collapse="-")
  #list('pageLength', list(extend='excel',title=dl_fname), list(extend='csv',title=dl_fname),'print','copy', 'colvis')
  list('pageLength', list(extend='csv',title=dl_fname),'print','copy', 'colvis')
}

## helper functions for loading the files reactively
##   file_glob_pattern contains %s, which is to be replaced by the sample names
list_kraken_files <- function(data_dir, file_names,file_extension,sample_name=NULL) {

  #file_paths <- paste0(data_dir, "/", file_names)
  sample_file_globs <- sapply(sample_name,
                              function(my_sample_name) gsub("%s",my_sample_name,file_glob_pattern)
                              )
  #if (is.null(sample_file_globs))
  info_message("Looking for files with pattern(s) ",paste(sample_file_globs,collapse=","))
  #list.files(data_dir,pattern=sample_file_globs,...)
  Sys.glob(paste0(data_dir,"/",sample_file_globs))
}

get_sample_name <- function(file_names, regex_pattern) {
  sapply(file_names, function(file_name) sub(regex_pattern,"\\1",file_name))
}

beautify_string <- function(x) {
  x <- gsub("[\\._]"," ",x)
  x <- sub("^([[:alpha:]])", "\\U\\1", x, perl=TRUE)
  x
}

beautify_taxLineage <- function(x, remove_last=TRUE, break_it_up = FALSE) {
  if (remove_last) {
    x <- sub("(.*)\\|.*","\\1",x)
  }
  x <- sub("^-_root.","", x)
  if (isTRUE(break_it_up)) {
    x <- gsub("\\|._", "<wbr>>", x)
  } else {
    x <- gsub("\\|._", ">", x)
  }
  x %>%
    sub("^._","", .) %>%
    gsub(" ", "&nbsp;", .) %>%
    gsub("-","&#x2011;", .)
}

text_representation <- function(my_report,
                                name_format=function(x) paste(x, collapse=">"),
                                reads_format=function(x, y) x,
                                min_reads = 0,
                                collapse="\n") {

  my_name <- sub("^._","",my_report$name)
  n <- nrow(my_report)
  res_depth <- c(); res_name <- c(); res_reads <- c(); res_plus <- c();

  has_plus = FALSE

  curr_name <- c()
  for (i in seq(from=n-1, to=1)) {
    curr_name <- c(my_name[i], curr_name)
    if (i == 1 ||
        my_report[i-1, "cladeReads"] != my_report[i, "cladeReads"] ||
        my_report[i-1, "depth"] != my_report[i, "depth"] - 1) {
      if (my_report[i, "cladeReads"] >= min_reads) {
        res_name <- c(name_format(curr_name),res_name)
        res_reads <- c(my_report[i, "cladeReads"], res_reads)
        res_depth <- c(my_report[i, "depth"], res_depth)
        res_plus <- c(ifelse(has_plus, "+", ""), res_plus)
        has_plus <- FALSE
      } else {
        has_plus <- TRUE
      }
      curr_name <- c()
    }
  }

  nn <- length(res_depth)
  if (nn < 1) {
      return();
  }

  space   <- "&nbsp;&nbsp;"
  vline   <- "&#9474;&nbsp;"
  cornerc <- "&#9500;&nbsp;"
  corner  <- "&#9492;&nbsp;"

  space   <- "&nbsp;"
  vline   <- "&#9474;"
  cornerc <- "&#9500;"
  corner  <- "&#9492;"


  res_path <- as.list(rep(NA, nn))
  res_path[[nn]] <- c(rep(space, res_depth[nn]), corner)
  for (i in seq(from=nn-1, to=1)) {
    my_path <- rep(space, res_depth[i])
    old_path <- res_path[[i+1]]
    old_path[length(old_path)] <- vline
    sel <- seq(from=1, to=min(length(old_path), length(my_path)))
    my_path[sel] <- old_path[sel]
    res_path[[i]] <- c(my_path,
                       ifelse(length(old_path) >= (length(my_path) + 1) &&
                              old_path[length(my_path) + 1] == vline, cornerc, corner))
  }
  #path <- sapply(res_depth, function(x) paste(rep(" ",x-1), collapse = ""))
  path <- sapply(res_path, function(x) { paste(x,collapse = ""); } )
  white_to_red <- grDevices::colorRampPalette(c("white", "red"))( 20 )
  #brks <- stats::quantile(my_report$cladeReads, probs = cumsum(1/2^(1:20)), na.rm =TRUE)
  brks <- stats::quantile(res_reads, probs = c(0,cumsum(1/2^(1:19))), na.rm =TRUE)
  int <- findInterval(res_reads, brks)


  HTML(paste0(sprintf("<span style='font-family: monospace;'>%s</span>%s%s %s", path, res_name, res_plus, reads_format(res_reads, white_to_red[int])), collapse = collapse))
}


#' Beautify colnames
#'
#' @param x data.frame or matrix
#'
#' @return data.frame or matrix with nicer colnames
#' @export
beautify_colnames <- function(x) {
  colnames(x) <- beautify_string(colnames(x))
  x
}

#' Helper function that sets NAs to zeros in a supplied data.frame
#'
#' @param df data.frame or matrix
#'
#' @return data.frame or matrix in which all negative and NA values are set to zero
#' @export
zero_if_na <- function(df) {
  stopifnot(!is.null(df))
  if (nrow(df) > 0) {
    df[is.na(df) | df < 0] <- 0
  }
  return(df)
}

styleColorBar2 = function(data, color, angle=90) {
  rg = range(data, na.rm = TRUE, finite = TRUE)
  r1 = rg[1]; r2 = rg[2]; r = r2 - r1
  htmlwidgets::JS(sprintf(
    "isNaN(parseFloat(value)) || value <= %s ? '' : 'linear-gradient(%sdeg, transparent ' + (%s - value)/%s * 100 + '%%, %s ' + (%s - value)/%s * 100 + '%%)'",
    r1, angle, r2, r, color, r2, r
  ))
}

# get directory listing for shinyTree
get_directory_listing <- function(my_dir) {
      all_dirs <- list.dirs(my_dir, recursive = FALSE, full.names=TRUE)
      all_dirs_short <- sub(".*/","",all_dirs)
      all_files <- list.files(my_dir)
      all_files <- all_files[!all_files %in% all_dirs_short]
      if (length(all_files) == 0 && length(all_dirs) == 0)
          return(structure(''))

      c(stats::setNames(lapply(all_dirs,get_directory_listing),all_dirs_short),
        stats::setNames(rep(structure('',sticon='file'),length(all_files)),all_files))
}

## only invalidate reactive when it's value changed
# from https://github.com/rstudio/shiny/issues/1484#issuecomment-262812760
dedupe <- function(r) {
  makeReactiveBinding("val")
  observe(val <<- r(), priority = 10)
  reactive(val)
}


now <- function() proc.time()[[3]]

# from http://stackoverflow.com/questions/11340444/is-there-an-r-function-to-format-number-using-unit-prefix
f2si2<-function (number)
{
  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")
  sel <- lut >= 1
  lut <- lut[sel]
  pre <- pre[sel]
  
  number[is.na(number)] <- 0
  
  ix <- findInterval(number, lut)
  ix[ix == 0] <- 1


  number2 <- signif(number/lut[ix],3)
  number2[number2 < 1] <- signif(number2[number2 < 1], 2)
  number2[number2 < .1] <- signif(number2[number2 < .1], 1)

  sistring <- sub("^0", "", paste0(number2,pre[ix]))

  return(sistring)
}

shinyTryCatch <- function(..., message = expression) {
  tryCatch(...,
           error=function(e) {
             full_message = sprintf("%s ERROR: %s (%s)",
                                    format(Sys.time(), "%D %H:%M"), message, e$message)
             stop(safeError(full_message))
             shiny::validate(need(FALSE, message=message))
           })
}

dmessage <- function(..., ID=NULL) {
  if (!is.null(ID)){
    ID <- get("pID")
    message("[",ID$val," ", format(Sys.time(), "%b%d %H:%M"),"] ",...)
  } else {
    message(format(Sys.time(), "[%b%d %H:%M]")," ",...)
  }
}

withProgress1 <- function(expr, ..., quoted=F, message=NULL) {
  if (!quoted)
    expr <- substitute(expr)
  
  withProgress(shinyTryCatch(expr, message=message), ..., quoted=F, message=message)
}

assert <- function(..., message = NULL) {
  tryCatch({
    stopifnot(...)
  }, error = function(e) {
    message <- paste0(format(Sys.time(), "%D %H:%M"),": ",message)
    stop(paste0(message,"\n",e$message))
  })
}