R/save.eigenplots.html.R

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

#' Generate HTML file for EigenFit plots
#'
#' @description Generate HTML file called 'tree_scree.html' from the result of
#' \code{\link{ipcaps2}}. This function is a part of workflow in
#' \code{\link{save.plots}}. 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{$output} object returned
#' from the \code{\link{ipcaps2}} function.
#'
#' @return \code{NULL}
#'
#' @details After running, this function generates the file called 'tree_scree.html' in the
#' same result directory. All plots are generated and saved as image files in
#' the sub-directory 'images'.
#'
#' @export
#'
#' @include output.template.R
#'
#' @seealso \code{\link{save.html}},
#' \code{\link{save.plots}},
#' \code{\link{save.plots.cluster.html}},
#' and \code{\link{save.plots.label.html}}
#'
#' @examples
#'
#' # Importantly, bed file, bim file, and fam file are required
#' # Use the example files embedded in the package
#'
#' BED.file <- system.file("extdata","ipcaps_example.bed",package="IPCAPS2")
#' LABEL.file <- system.file("extdata","ipcaps_example_individuals.txt.gz",package="IPCAPS2")
#'
#' my.cluster <- ipcaps2(bed=BED.file,
#'                       label.file=LABEL.file,
#'                       lab.col=2,
#'                       out=tempdir(),
#'                       silence=TRUE,
#'                       no.rep=1)
#'
#' #Here, to generate HTML file
#' save.eigenplots.html(my.cluster$output.dir)


save.eigenplots.html <- function(output.dir)
{
  tree <- NULL
  index <- NULL
  min.in.group <- NULL
  leaf.node <- NULL
  label <- NULL

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

  txt_data <- ""
  txt_leafnode <- ""

  test.dir <- file.path(output.dir, "images.new")
  img.dir <- "images"
  if (file.exists(test.dir))
  {
    img.dir <- "images.new"
  }

  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)
    list.sum <- c()
    u.label <- sort(unique(label))
    for (j in seq(1, length(u.label)))
    {
      co <- length(label[label == u.label[j]])
      strout <- paste0(u.label[j], "&nbsp;(", co, ")")
      list.sum <- c(list.sum, strout)
    }
    content <- ""
    for (s in list.sum)
    {
      content <- paste0(content, s, "<br>")
    }
    if (file.exists(file.path(
      output.dir,
      "images",
      paste0("eigenvalue_preview",
             i, ".jpg")
    )))
    {
      txt_data <- paste0(
        txt_data,
        "[{v:'",
        i,
        "', f:'<div class=\"box_class\" align=\"center\">",
        "<p class=\"head_class\">Node ",
        i,
        "</p><a href=\"",
        img.dir,
        "/eigenvalue",
        i,
        ".png\" target=\"_blank\"><img src=\"",
        img.dir,
        "/eigenvalue_preview",
        i,
        ".jpg\" width=200 height=200>",
        "<br />view</a></div>'}, '",
        parent_node,
        "', '']"
      )
    } else if (file.exists(file.path(
      output.dir,
      "images",
      paste0("eigenvalue_preview",
             i, ".pdf")
    )))
    {
      txt_data <- paste0(
        txt_data,
        "[{v:'",
        i,
        "', f:'<div class=\"box_class\" align=\"center\">",
        "<p class=\"head_class\">Node ",
        i,
        "</p><a href=\"",
        img.dir,
        "/eigenvalue",
        i,
        ".pdf\" target=\"_blank\"><embed src=\"",
        img.dir,
        "/eigenvalue_preview",
        i,
        ".pdf\" width=200 height=200>",
        "<br />view</a></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 <- "Scree plots of Eigen values"
  txt_body <- "Scree plots of Eigen values"

  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_scree.html"), "w")
  for (i in txt_html)
  {
    write(i, fo)
  }
  close(fo)

  invisible(NULL)
}