R/save.html.R

In kridsadakorn/ipcaps2: Iterative Pruning to Capture Population Structure version 2

#' Generate HTML file for clustering result in text mode
#'
#' @description Generate HTML file called 'tree_text.html' from the result of
#' \code{\link{ipcaps2}}. The clustering result is shown as a tree rendering by
#' the online Google Organizational Chart library. Note that the Internet is
#' required to view the HTML file.
#'
#' @param output.dir A result directory as the \code{$output} object returned
#' from the \code{\link{ipcaps2}} function.
#'
#' @return \code{NULL}
#'
#' @details After running, this function generates the file called 'tree_text.html' in the
#' same result directory.
#'
#' @export
#'
#' @include output.template.R
#'
#' @seealso \code{\link{save.plots}},
#' \code{\link{save.plots.cluster.html}},
#' \code{\link{save.eigenplots.html}},
#' and \code{\link{save.plots.label.html}}
#'
#' @examples
#'
#' # Importantly, bed file, bim file, and fam file are required
#' # Use the example files embedded in the package
#'
#' BED.file <- system.file("extdata","ipcaps_example.bed",package="IPCAPS2")
#' LABEL.file <- system.file("extdata","ipcaps_example_individuals.txt.gz",package="IPCAPS2")
#'
#' my.cluster <- ipcaps2(bed=BED.file,
#'                       label.file=LABEL.file,
#'                       lab.col=2,
#'                       out=tempdir(),
#'                       silence=TRUE,
#'                       no.rep=1)
#'
#' #Here, to generate HTML file
#' save.html(my.cluster$output.dir)

save.html <- function(output.dir)
{
  tree <- NULL
  index <- NULL
  eigen.fit <- NULL
  min.in.group <- NULL
  leaf.node <- NULL
  threshold <- NULL

  load(file.path(output.dir, "RData", "leafnode.RData"))
  load(file.path(output.dir, "RData", "condition.RData"))
  load(file.path(output.dir, "RData", "tree.RData"))
  load(file.path(output.dir, "RData", "rawdata.RData"))
  global.label <- label
  node.list <- sort(tree$node)

  txt_data <- ""
  txt_leafnode <- ""
  for (i in node.list)
  {
    parent_node <- ""
    if (i > 1)
    {
      parent_node <- tree$parent.node[which(tree$node == i)]
    }
    PCs.file <-
      file.path(output.dir, "RData", paste0("node", i, ".RData"))
    load(PCs.file)
    label <- global.label[index]
    list.sum <- c()
    u.label <- sort(unique(label))
    for (j in seq(1, length(u.label)))
    {
      co <- length(label[label == u.label[j]])
      strlabel <- gsub(" ", "&nbsp;", u.label[j])
      strout <- paste0(strlabel, "&nbsp;(", co, ")")
      list.sum <- c(list.sum, strout)
    }
    content <- ""
    for (s in list.sum)
    {
      content <- paste0(content, s, "<br>")
    }
    if (!is.na(eigen.fit))
    {
      txt_data <- paste0(
        txt_data,
        "[{v:'",
        i,
        "', f:'<div class=\"box_class\">",
        "<p class=\"head_class\">Node ",
        i,
        "</p><p class=\"subhead_class\">EigenFit= ",
        sprintf("%.2f", eigen.fit),
        "</p><br>",
        content,
        "</div>'}, '",
        parent_node,
        "', '']"
      )
    } else
    {
      txt_data <- paste0(
        txt_data,
        "[{v:'",
        i,
        "', f:'<div class=\"box_class\">",
        "<p class=\"head_class\">Node ",
        i,
        "</p><p class=\"subhead_class\">under cutoff (<",
        min.in.group,
        ")</p><br>",
        content,
        "</div>'}, '",
        parent_node,
        "', '']"
      )
    }
    if (!(i == node.list[length(node.list)]))
    {
      txt_data <- paste0(txt_data, ",\n")
    } else
    {
      txt_data <- paste0(txt_data, "\n")
    }

    no_idx <- which(i == node.list) - 1
    if (i %in% leaf.node)
    {
      txt_leafnode <- paste0(
        txt_leafnode,
        "data.setRowProperty(",
        no_idx,
        ", 'style', 'border: 3px solid #DB6E6E; ",
        "background-color:#FFE1E1');\n"
      )
    }
  }

  txt_title <- "The result of ipcaps"
  txt_body <- paste0("The result of ipcaps (threshold= ", threshold,
                     ")")

  txt_html <- output.template$template
  txt_html[output.template$lno_data] <- txt_data
  txt_html[output.template$lno_leafnode] <- txt_leafnode
  txt_html[output.template$lno_body] <- txt_body
  txt_html[output.template$lno_title] <- txt_title

  fo <- file(file.path(output.dir, "tree_text.html"), "w")
  for (i in txt_html)
  {
    write(i, fo)
  }
  close(fo)

  invisible(NULL)
}