R/rewiring_html_summary_functions.R

In ubioinformat/TraRe: Transcriptional Rewiring

#' Generate html report from the `runrewiring()` method.
#'
#' @description
#'
#' Contain functions to generate an html report from the rewired linker modules.
#' `create_index_page()` initializes folders and files for the html report. `write_tables_all()` generates
#' a table given stats from the rewiring method. `write_html_table_page()` creates the header for the
#' html file when the table will be placed. `table2html()` gets the `write_html_table_page()` info and
#' return the generated html file. This functions run inside `runrewiring()`
#'
#' @param outdir path for the resultant folder.
#' @param runtag name that is `paste()` to the name folder.
#' @param codedir folder from which `sorttable.js` and `glossary.txt`
#' files are `paste()` into the output folder.
#' @param indexpath name for the index file.
#' @param glossarypath name for the glossary file.
#' @param imgstr path for the image folder.
#' @param txtstr path for the txts folder.
#'
#' @param mytab table to transform into html file.
#' @param tabletype type of table.
#' @param html_idxs index for table rows.
#' @param html_cols index for table columns.
#' @param filestr name of the html file to be generated.
#' @param htmlinfo list containing `indexpath`,`txtstr`, and html dir.
#'
#'
#' @param resultstable modified table from `write_tables_all()`.
#' @param htmlpagefile path of the html file.
#' @param resultsrelpath path of the txt files.
#'
#'
#'
#' @noRd


table2html_from_graph <- function(resultstable, numvar = TRUE) {

    if (numvar) {
        numvar <- "idx"
    } else {
        numvar <- "Drivers"
    }

    colheader <- paste(collapse = "</th><th>", c(numvar, colnames(resultstable)))
    theader <- paste0("<thead>\n<tr bgcolor='#AAAAAA';><th>", colheader, "</th></tr>\n</thead>\n<tbody>\n")
    head_str <- paste0("<script src='../../sorttable.js'></script>\n<TABLE class=", "'sortable' border =1 >\n", theader)
    
    numtable <- cbind(rownames(resultstable), resultstable)
    rowinnerstrs <- apply(numtable, 1, paste, collapse = "</td><td>")
    rowstrs <- paste0("<tr><td>", rowinnerstrs,"</td></tr>")
    rows_str <- paste(collapse = "\n", rowstrs)

    return(paste0(collapse = "\n", head_str, rows_str, "\n</tbody></table><br>"))


}

table2html <- function(resultstable) {

    colheader <- paste(collapse = "</th><th>", c("idx", colnames(resultstable)))
    theader <- paste0("<thead>\n<tr bgcolor='#AAAAAA';><th>", colheader, "</th></tr>\n</thead>\n<tbody>\n")
    head_str <- paste0("<script src='../sorttable.js'></script>\n<TABLE class=", "'sortable' border =1 >\n", theader)

    numtable <- cbind(seq_len(nrow(resultstable)), resultstable)
    rowinnerstrs <- apply(numtable, 1, paste, collapse = "</td><td>")
    rowstrs <- paste0("<tr><td>", rowinnerstrs, "</td></tr>")
    rows_str <- paste(collapse = "\n", rowstrs)

    return(paste0(collapse = "\n", head_str, rows_str, "\n</tbody></table><br>"))

}


write_html_table_page <- function(resultstable, htmlpagefile, resultsrelpath, indexpath = "index.html", glossarypath = "glossary.txt",
    htmlinfo) {

    write(paste0("<table border = 1 width = '100%'><tr bgcolor = ", "'#AAAAAA'><th><a href = '", "../", indexpath, "'>",
        "Index</a></th><th><a href = '"," ../",glossarypath, "' >", "Glossary</a></th><th><a href = '",
        "../", resultsrelpath, "' >Download</a></th></tr></table><br><br>"), file = htmlpagefile)
    htmlstr <- table2html(resultstable)
    write(htmlstr, file = htmlpagefile, append = TRUE)

}


write_tables_all <- function(mytab, tabletype = "table", html_idxs = seq_len(nrow(mytab)), html_cols = colnames(mytab), filestr = "data",
    htmlinfo = list(htmldir = "htmls/", indexpath = "index.html", txtstr = "txts/",abspath="./"), extradir = "", glossarypath = "glossary.txt") {


    htmlpath <- paste0("htmls/", filestr, "_", tabletype, ".html")
    resultspath <- paste0(htmlinfo$txtstr, filestr, "_", tabletype, ".txt")
    message("Writing table: ", extradir, resultspath)
    # Write the table as .txt
    utils::write.table(mytab, paste0(htmlinfo$htmldir, extradir, resultspath), sep = "\t", row.names = FALSE, col.names = TRUE, quote = FALSE)

    # Write hyperlink in index file
    write(paste0("<a href = \"", htmlpath, "\">", tabletype, "</a><br>"), file = paste0(htmlinfo$htmldir, extradir,
        htmlinfo$indexpath), append = TRUE)

    # Write the table in .html format
    write_html_table_page(resultstable = mytab[html_idxs, html_cols], htmlpagefile = paste0(htmlinfo$htmldir, extradir, htmlpath),
        resultsrelpath = resultspath, indexpath = htmlinfo$indexpath, glossarypath = glossarypath, htmlinfo = htmlinfo)
}

create_index_page <- function(outdir = "./", runtag = "run", codedir = "code/", indexpath = "index.html", glossarypath = "glossary.txt",
    imgstr = "imgs/", txtstr = "txts/", htmlstr = "htmls/", report_name="") {

    htmldir <- paste0(outdir, runtag, "/")
    dir.create(file.path(htmldir))

    file.copy(from = paste0(codedir, "sorttable.js"), to = htmldir)

    # Create folder imgs
    dir.create(file.path(paste0(htmldir, imgstr)))

    # Create folder txts
    dir.create(file.path(paste0(htmldir, txtstr)))

    # Create folder htmls
    dir.create(file.path(paste0(htmldir, htmlstr)))

    # glossary <- as.matrix(utils::read.table(paste0(codedir, "glossary.txt"), header = TRUE, sep = "\t", quote = ""))
    file.copy(from = paste0(codedir, "glossary.txt"), to = htmldir)
    abspath <- paste0(htmldir, indexpath)

    write(paste0("<br>"), file = abspath)

    return(list(htmldir = htmldir, indexpath = indexpath, imgstr = imgstr, txtstr = txtstr, glossarypath = glossarypath, abspath = abspath,report_name=report_name))
}

violinPlots <- function(norm_expr_mat_keep, phenosamples, pheno, nodesumm, edgesumm, objtargs, htmlinfo) {

    modhtmlfile <- paste0(htmlinfo$htmldir, htmlinfo$indexpath)
    imgdir <- paste0(htmlinfo$htmldir, htmlinfo$imgstr)

    normexpmat <- norm_expr_mat_keep[, phenosamples]
    nodesumm2 <- utils::type.convert(as.data.frame(nodesumm, stringsAsFactors = FALSE))
    colnames(nodesumm2) <- make.names(colnames(nodesumm2))

    reg_info <- nodesumm2[nodesumm2$is.regulator == 1, c("t.stat", "t.pval")]
    reg_info <- reg_info[order(reg_info$t.stat, decreasing = TRUE), ]
    reg_vec <- rownames(reg_info)

    # --- regulator expression distributions ---
    write(paste0("<table style='width:100%' bgcolor='gray'><tr><td><h1>", "Regulator Expression Levels", "</h1></td></tr></table><br>\n"),
        modhtmlfile, append = TRUE)

    respond_plotlist <- list()
    nonresp_plotlist <- list()
    for (reg in reg_vec) {
        respond_plotlist[[reg]] <- as.numeric(normexpmat[reg, pheno == 1])
        nonresp_plotlist[[reg]] <- as.numeric(normexpmat[reg, pheno == 0])
        # methods::show(c(reg, signif(mean(respond_plotlist[[reg]])), signif(mean(nonresp_plotlist[[reg]]))))
    }

    plotwidth <- 500
    plotheight <- 800
    myplotname <- paste0("violin.regexp")

    grDevices::png(paste0(imgdir, myplotname, ".png"), width = plotwidth, height = plotheight)

    vioplot::vioplot(x = respond_plotlist, col = "palevioletred", side = "right", names = paste(sep = "||", rownames(reg_info), signif(reg_info$t.pval,
        2)), plotCentre = "line", horizontal = TRUE, cex.axis = 0.8)

    vioplot::vioplot(x = nonresp_plotlist, col = "lightblue", side = "left", add = TRUE, plotCentre = "line", horizontal = TRUE)

    graphics::abline(v = -5:5 * 2, col = "lightgrey")
    graphics::title(xlab = "Expression Value (CQN)", ylab = "Regulator")

    graphics::legend("topleft", fill = c("palevioletred", "lightblue"), legend = c("R", "NR"), title = "Outcome", cex = 0.5)
    grDevices::dev.off()

    rankdf <- data.frame(matrix(vector(), length(reg_vec), 0, dimnames = list(sample(reg_vec), c())), stringsAsFactors = FALSE)
    rankdfcols <- c()
    rankdfcols <- c(rankdfcols, "regulator", "reg.expr.tpval", "reg.expr.rank")
    rankdf <- cbind(rankdf[rownames(reg_info), ], rownames(reg_info), signif(reg_info$t.pval, 2), rank(reg_info$t.pval))
    colnames(rankdf) <- rankdfcols

    write(paste0("<img src='", htmlinfo$imgstr, myplotname, ".png", "' alt='", myplotname, "' height='", plotheight, "' width='", plotwidth,
        "'><br>\n"), modhtmlfile, append = TRUE)

    # --- target expression diff distributions ---
    write(paste0("<table style='width:100%' bgcolor='gray'><tr><td><h1>", "Target Expression Diff Distributions", "</h1></td></tr></table><br>\n"),
        modhtmlfile, append = TRUE)
    write("<table style='width:100%'> ", modhtmlfile, append = TRUE)
    write(paste0("<tr>"), modhtmlfile, append = TRUE)

    for (cname in c("all", "nonresp", "respond")) {
        nonzeroedges <- edgesumm[edgesumm[, paste0(cname, ".weights")] != 0, ]
        plotlist <- list()
        for (reg in reg_vec) {
            # targets <- as.character(nonzeroedges[nonzeroedges$reg == reg, "target"])
            targets <- intersect(as.character(nonzeroedges[nonzeroedges$reg == reg, "target"]), objtargs)
            plotlist[[reg]] <- as.numeric(nodesumm2[targets, "t.stat"])
            # methods::show(c(reg, length(targets), signif(mean(plotlist[[reg]]))))
        }
        plotlist <- plotlist[names(sort(unlist(lapply(plotlist, mean)), decreasing = TRUE))]
        plotlist[["supmod"]] <- as.numeric(nodesumm2[, "t.stat"])

        # added png
        plotwidth <- 500
        plotheight <- 800
        myplotname0 <- paste0("violin.tarexpdiff.", cname)

        grDevices::png(paste0(imgdir, myplotname0, ".png"), width = plotwidth, height = plotheight)

        vioplot::vioplot(x = plotlist, col = "goldenrod", side = "right", main = cname, names = paste(sep = "||", names(plotlist),
            unlist(lapply(plotlist, length)), signif(unlist(lapply(plotlist, mean)), 3)), plotCentre = "line", horizontal = TRUE, cex.axis = 0.6)

        graphics::abline(v = -5:5 * 2, col = "lightgrey")
        graphics::title(xlab = "T Statistic: Higher in Responders <-> Not Signficant <-> Higher in Non-Responders", ylab = "Regulator Targets")
        grDevices::dev.off()

        if (cname == "all") {
            rankdfcols <- c(rankdfcols, "all.targets", "tar.diffexpr.avg", "tar.diffexpr.rank")
            tmpvals <- signif(unlist(lapply(plotlist, mean)), 3)[reg_vec]
            rankdf <- cbind(rankdf[reg_vec, ], unlist(lapply(plotlist, length))[reg_vec], tmpvals, rank(tmpvals))
            colnames(rankdf) <- rankdfcols
        }

        write(paste0(" <img src='", htmlinfo$imgstr, myplotname0, ".png", "' alt='", myplotname0, "' height='", plotheight, "' width='",
            plotwidth, "'> &emsp; \n"), modhtmlfile, append = TRUE)
    }
    write(paste0("</tr>\n"), modhtmlfile, append = TRUE)
    write(paste0("</table>"), modhtmlfile, append = TRUE)

    # --- target regulator correlation distributions ---
    write(paste0("<table style='width:100%' bgcolor='gray'><tr><td><h1>", "Target Regulator Correlation Distributions", "</h1></td></tr></table><br>\n"),
        modhtmlfile, append = TRUE)
    write("<table style='width:100%'> ", modhtmlfile, append = TRUE)
    write(paste0("<tr>"), modhtmlfile, append = TRUE)

    # calculate module correlation
    modmat <- t(normexpmat[rownames(nodesumm2), ])
    corall <- stats::cor(modmat)
    corR <- stats::cor(modmat[pheno == 1, ])
    corNR <- stats::cor(modmat[pheno == 0, ])
    corR[is.na(corR)] <- 0
    corNR[is.na(corNR)] <- 0
    cordiff <- corNR - corR

    for (loopmode in c("all", "specific")) {
        # plot regulator target set correlation
        respond_plotlist <- list()
        nonresp_plotlist <- list()
        mypvals <- rep(2, length(reg_vec))
        names(mypvals) <- reg_vec

        for (reg in reg_vec) {
            respondtars <- as.character(edgesumm$target[edgesumm$respond.weights != 0 & edgesumm$reg == reg])
            nonresptars <- as.character(edgesumm$target[edgesumm$nonresp.weights != 0 & edgesumm$reg == reg])
            if (loopmode == "all") {
                respondtars <- as.character(edgesumm$target[edgesumm$all.weights != 0 & edgesumm$reg == reg])
                nonresptars <- as.character(edgesumm$target[edgesumm$all.weights != 0 & edgesumm$reg == reg])
            }
            respondtars <- intersect(respondtars,objtargs)
            nonresptars <- intersect(nonresptars,objtargs)
            respond_plotlist[[reg]] <- as.numeric(corR[reg, respondtars])
            nonresp_plotlist[[reg]] <- as.numeric(corNR[reg, nonresptars])

            if (length(respondtars) < 2 | length(nonresptars) < 2) {
                mypvals[reg] <- 1
                respond_plotlist[[reg]] <- 0
                nonresp_plotlist[[reg]] <- 0

            } else if (stats::var(respond_plotlist[[reg]]) == 0 | stats::var(nonresp_plotlist[[reg]]) == 0) {
                mypvals[reg] <- 1

            } else {
                tres <- stats::t.test(respond_plotlist[[reg]], nonresp_plotlist[[reg]])
                mypvals[reg] <- signif(tres$p.value, 1)
            }
            # methods::show(c(reg, length(respondtars), length(nonresptars), signif(mean(respond_plotlist[[reg]])), signif(mean(nonresp_plotlist[[reg]])),
            # as.numeric(mypvals[reg])))
        }
        respond_plotlist <- respond_plotlist[names(sort(mypvals, decreasing = TRUE))]
        nonresp_plotlist <- nonresp_plotlist[names(sort(mypvals, decreasing = TRUE))]
    }

    for (loopmode in c("all", "specific")) {
        # plot histogram of target/regulator correlation
        plotwidth <- 500
        plotheight <- 800
        myplotname <- paste0("violin.tarregcorr.", loopmode)

        grDevices::png(paste0(imgdir, myplotname, ".png"), width = plotwidth, height = plotheight)

        vioplot::vioplot(x = respond_plotlist, col = "palevioletred", side = "right", main = loopmode, names = paste(sep = "||", names(respond_plotlist),
            unlist(lapply(respond_plotlist, length)), unlist(lapply(nonresp_plotlist, length)), mypvals[names(respond_plotlist)]),
            plotCentre = "line", horizontal = TRUE, cex.axis = 0.6)

        vioplot::vioplot(x = nonresp_plotlist, col = "lightblue", side = "left", add = TRUE, plotCentre = "line", horizontal = TRUE)

        graphics::abline(v = -5:5/5, col = "lightgrey")
        graphics::title(xlab = "Pearson Correlation", ylab = "Regulator Targets")

        graphics::legend("topleft", fill = c("palevioletred", "lightblue"), legend = c("R", "NR"), title = "Outcome", cex = 0.5)
        grDevices::dev.off()

        if (loopmode == "all") {
            rankdfcols <- c(rankdfcols, "regtar.corr.tpval", "regtar.corr.rank")
            rankdf <- cbind(rankdf[names(mypvals), ], mypvals, rank(mypvals))
            colnames(rankdf) <- rankdfcols
        }

        write(paste0("<img src='", htmlinfo$imgstr, myplotname, ".png", "' alt='", myplotname, "' height='", plotheight, "' width='",
            plotwidth, "'> &emsp; \n"), modhtmlfile, append = TRUE)
    }
    write(paste0("</tr>\n"), modhtmlfile, append = TRUE)
    write(paste0("</table>"), modhtmlfile, append = TRUE)

    return(rankdf)
}

bipartiteGraphsSumm <- function(numclus, nodesumm, edgesumm, numdataset, modmeth, htmlinfo) {
  modhtmlfile <- paste0(htmlinfo$htmldir, htmlinfo$indexpath)
  imgdir <- paste0(htmlinfo$htmldir, htmlinfo$imgstr)
  
  write(paste0("<table style='width:100%' bgcolor='gray'><tr><td><h1>", "Modules Summary", "</h1></td></tr></table><br>\n"), modhtmlfile,
        append = TRUE)
  
  pname <- paste(sep = ".", "igraphs.refined.graphs")
  # write plot to index page
  write(paste0("<embed src='", "../../supermodule", numdataset, ".", modmeth, ".", numclus, "/imgs/", pname, ".pdf", "' alt='", pname,
               "' height='", 750, "' width='", 1500, "'> &emsp; <br>\n"), modhtmlfile, append = TRUE)
  
  sortidxs <- sort(as.numeric(nodesumm[, "t-pval"]), decreasing = FALSE, index.return = TRUE)$ix
  #write_tables_all(nodesumm[sortidxs, ], tabletype = paste0(modmeth, "_nodesumm"), filestr = "data", html_idxs = 1:dim(nodesumm)[1],
  write_tables_all(nodesumm[sortidxs, ], tabletype = paste0(modmeth, "_nodesumm"), filestr = "data", html_idxs = seq(nrow(nodesumm)),
                   htmlinfo = htmlinfo)
  
  sortidxs <- sort(as.numeric(edgesumm[, "all-pearson"]), decreasing = FALSE, index.return = TRUE)$ix
  #write_tables_all(edgesumm[sortidxs, ], tabletype = paste0(modmeth, "_edgesumm"), filestr = "data", html_idxs = 1:dim(edgesumm)[1],
  write_tables_all(edgesumm[sortidxs, ], tabletype = paste0(modmeth, "_edgesumm"), filestr = "data", html_idxs = seq(nrow(edgesumm)),
                   htmlinfo = htmlinfo)
  
}

geneOrder <- function(modsumm, ObjectList, numdataset) {
  allregs<- ObjectList$datasets[[numdataset]]$regs
  alltargs<- ObjectList$datasets[[numdataset]]$targs
  pheno <- ObjectList$datasets[[numdataset]]$pheno
  phenosamples <- ObjectList$datasets[[numdataset]]$phenosamples
  lognorm_est_counts <- ObjectList$datasets[[numdataset]]$lognorm_est_counts
  
  modregs <- intersect(unique(modsumm$fulledgesumm$reg),allregs)
  modtargs <- intersect(unique(modsumm$fulledgesumm$target),alltargs)
  difftargs <- setdiff(unique(modsumm$fulledgesumm$target),alltargs)
  diffregs <- setdiff(unique(modsumm$fulledgesumm$reg),allregs)
  if (length(diffregs) != 0) {
    message('List of regulators changed since ', length(diffregs),' regulators in the dataset that was used to generate runrewiring is missing in dataset ', numdataset, '.')
  }
  if (length(difftargs) != 0) {
    message('List of targets changed since ', length(difftargs),' targets in the dataset that was used to generate runrewiring is missing in dataset ', numdataset, '.')
  }
  
  
  keepfeat <- unique(c(modregs, modtargs))
  mat <- t(lognorm_est_counts[keepfeat, phenosamples])
  
  # calculate correlation matrices
  corall <- stats::cor(mat)
  cor1 <- stats::cor(mat[(pheno + 1) == 1, seq(ncol(mat))])
  cor2 <- stats::cor(mat[(pheno + 1) == 2, seq(ncol(mat))])
  
  cor1[is.na(cor1)] <- 0
  cor2[is.na(cor2)] <- 0
  cordiff <- cor1 - cor2
  cormats <- list(corall = corall, cordiff = cordiff, cor1 = cor1, cor2 = cor2)
  
  # order genes by clustering of corrdiff
  targetorder <- labels(stats::as.dendrogram(stats::hclust(stats::dist(cordiff[modtargs, modtargs]))))
  regorder <- modregs
  if (length(modregs) > 1) {
    regorder <- labels(stats::as.dendrogram(stats::hclust(stats::dist(cordiff[modregs, modregs]))))
  }
  
  return(list(modregs = modregs, modtargs = modtargs, mat = mat, targetorder = targetorder, regorder = regorder, cormats = cormats))
}


superModuleStatistics <- function(modregs, modtargs, mat, pheno, htmlinfo) {
    modhtmlfile <- paste0(htmlinfo$htmldir, htmlinfo$indexpath)

    regnames <- paste(collapse = ", ", modregs)
    split <- as.numeric(table(pheno))
    stats <- c(length(modtargs), length(modregs), regnames, dim(mat), split)

    statsnames <- c("num-targets", "num-regulators", "regulator-names", "num-samples", "num-genes", "num-pheno0", "num-pheno1")

    stattab <- cbind(statsnames, stats)

    write(paste0("<table style='width:100%' bgcolor='gray'><tr><td><h1>", "SuperModule Statistics", "</h1></td></tr></table><br>\n"),
        paste0(htmlinfo$htmldir, htmlinfo$indexpath), append = TRUE)
    write(table2html(stattab), modhtmlfile, append = TRUE)
}

createLegendPlot <- function(htmlinfo,type, mat) {
  imgdir <- paste0(htmlinfo$htmldir, htmlinfo$imgstr)
  
  plotwidth <- 450
  plotheight <- 150
  if(type==1){
    myplotname <- paste0("correlation_colorscale")
    grDevices::png(paste0(imgdir, myplotname, ".png"), width = plotwidth, height = plotheight)
    ngroups <- 9
    vals <- seq(-1, 1, length.out = ngroups)
    
    colramp <- (grDevices::colorRampPalette(c("darkred", "gray100", "darkgreen")))(ngroups)
    graphics::image(vals, 1, as.matrix(vals, ngroups, 1), col = colramp, axes = FALSE, main = "", xlab = "", ylab = "")
    graphics::axis(1, vals, cex.axis = 2)
    grDevices::dev.off()
  }
  if (type==2){
    myplotname <- paste0("expression_colorscale")
    grDevices::png(paste0(imgdir, myplotname, ".png"), width = plotwidth, height = plotheight)
    ngroups <- sqrt(length(mat))
    min_exp_value <- signif(min(mat),2)
    max_exp_value <- signif(max(mat),2)
    plotzlim <- c(min_exp_value,max_exp_value)
    vals <- seq(min_exp_value, max_exp_value, length.out = ngroups)
    
    colramp <- (grDevices::colorRampPalette(c("darkorange", "gray100", "darkblue")))(ngroups)
    graphics::image(vals, 1, as.matrix(vals, ngroups, 1), col = colramp, axes = FALSE, main = "", xlab = "", ylab = "")
    graphics::axis(1, signif(seq(min_exp_value,max_exp_value,length.out=9),3), cex.axis = 1, at = signif(seq(min_exp_value,max_exp_value,length.out=9),3))
    grDevices::dev.off()
    return(plotzlim)
  }
}

# plot target correlation
correlationOfModuleGene <- function(mymod, regorder, targetorder, mat, cormats, htmlinfo, phenotype_class_vals) {
    modhtmlfile <- paste0(htmlinfo$htmldir, htmlinfo$indexpath)
    imgdir <- paste0(htmlinfo$htmldir, htmlinfo$imgstr)

    write(paste0("<table style='width:100%' bgcolor='gray'><tr><td><h1>", "Correlation Of Module Genes ", "</h1></td></tr></table><br>\n"),
        modhtmlfile, append = TRUE)

    write(paste0("<img src='", htmlinfo$imgstr, "correlation_colorscale", ".png", "' alt='", "correlation_colorscale", "' height='",
        150, "' width='", 450, "'><br>\n"), modhtmlfile, append = TRUE)

    write("<table style='width:100%'> ", modhtmlfile, append = TRUE)
    plot_correlation_row(cormats = cormats, rowdesc = "targets", xnames = targetorder, ynames = targetorder, plotheight = 450, myshowrows = TRUE,
        htmlfile = modhtmlfile, imgdir = imgdir, modnum = mymod, plotwidth = 450, mycvec = c("darkred", "gray100", "darkgreen"), plotzlim = c(-1,
            1), plottitle = phenotype_class_vals)


    # plot regulator correlation
    plot_correlation_row(cormats = cormats, rowdesc = "regulators", xnames = regorder, ynames = regorder, plotheight = 350, myshowrows = TRUE,
        htmlfile = modhtmlfile, imgdir = imgdir, modnum = mymod, plotwidth = 350, mycvec = c("darkred", "gray100", "darkgreen"), plotzlim = c(-1,
            1), plottitle = phenotype_class_vals)

    # plot regulator by target correlation
    plot_correlation_row(cormats = cormats, rowdesc = "all", xnames = targetorder, ynames = regorder, plotheight = 450, myshowrows = TRUE,
        htmlfile = modhtmlfile, imgdir = imgdir, modnum = mymod, plotwidth = 200, mycvec = c("darkred", "gray100", "darkgreen"), plotzlim = c(-1,
            1), plottitle = phenotype_class_vals)

    write(paste0("</table>"), modhtmlfile, append = TRUE)

}

expressionTableOfModuleGenes <- function(mymod, nodesumm, htmlinfo) {
    modhtmlfile <- paste0(htmlinfo$htmldir, htmlinfo$indexpath)

    write(paste0("<table style='width:100%' bgcolor='gray'><tr><td><h1>", "Expression Table of Module Genes", "</h1></td></tr></table><br>\n"),
        modhtmlfile, append = TRUE)

    sortidxs <- sort(as.numeric(nodesumm[, "t-pval"]), decreasing = FALSE, index.return = TRUE)$ix
    #htmlidxs <- union(sortidxs[1:25], which(nodesumm[, "is-regulator"] == "1"))
    htmlidxs <- union(sortidxs[seq(25)], which(nodesumm[, "is-regulator"] == "1"))
    write(table2html(nodesumm[htmlidxs, ]), modhtmlfile, append = TRUE)

    sortidxs <- sort(as.numeric(nodesumm[, "t-stat"]), decreasing = FALSE, index.return = TRUE)$ix
    #write_tables_all(nodesumm[sortidxs, ], tabletype = paste0(mymod, "_mod_node_summ"), filestr = "data", html_idxs = 1:dim(nodesumm)[1],
    write_tables_all(nodesumm[sortidxs, ], tabletype = paste0(mymod, "_mod_node_summ"), filestr = "data", html_idxs = seq(nrow(nodesumm)),
        htmlinfo = htmlinfo)
}

expressionPlotsOfModuleGenes <- function(mymod, regorder, targetorder, mat, samps2pheno, phenostrs, htmlinfo,plotzlim) {
  modhtmlfile <- paste0(htmlinfo$htmldir, htmlinfo$indexpath)
  imgdir <- paste0(htmlinfo$htmldir, htmlinfo$imgstr)
  
  write(paste0("<table style='width:100%' bgcolor='gray'><tr><td><h1>", "Expression Plots of Module Genes ", "</h1></td></tr></table><br>\n"),
        modhtmlfile, append = TRUE)
  
  write(paste0("<img src='", htmlinfo$imgstr, "expression_colorscale", ".png", "' alt='", "correlation_colorscale", "' height='",
               150, "' width='", 450, "'><br>\n"), modhtmlfile, append = TRUE)
  
  write("<table style='width:100%'> ", modhtmlfile, append = TRUE)
  
  # plot regulator expression
  plot_expression_row(mymat = t(mat)[regorder, , drop = FALSE], rowdesc = "regulators", plotheight = 400, myshowrows = TRUE, samps2pheno = samps2pheno,
                      phenostrs = phenostrs, htmlfile = modhtmlfile, imgdir = imgdir, modnum = mymod, plotwidth = 800, mycvec = c("darkorange", "gray100",
                                                                                                                                  "darkblue"), plotzlim = plotzlim)
  
  # plot target expression
  plot_expression_row(mymat = t(mat)[targetorder, ], rowdesc = "targets", plotheight = 600, myshowrows = TRUE, samps2pheno = samps2pheno,
                      phenostrs = phenostrs, htmlfile = modhtmlfile, imgdir = imgdir, modnum = mymod, plotwidth = 800, mycvec = c("darkorange", "gray100",
                                                                                                                                  "darkblue"), plotzlim = plotzlim)
  write(paste0("</table>"), modhtmlfile, append = TRUE)
}

nullDistributionOfRewiringStatistic <- function(mat, pheno, modmeth, mymod, htmlinfo) {
  modhtmlfile <- paste0(htmlinfo$htmldir, htmlinfo$indexpath)
  imgdir <- paste0(htmlinfo$htmldir, htmlinfo$imgstr)
  
  result <- NULL
  result <- rewiring_test_pair_detail(mat, pheno + 1, perm = 1000)
  
  write(paste0("<table style='width:100%' bgcolor='gray'><tr><td><h1>", "Null Distribution of Rewiring Statistic", "</h1></td></tr></table><br>\n"),
        modhtmlfile, append = TRUE)
  
  # plot histogram of dave stats
  plotwidth <- 400
  plotheight <- 400
  # myplotname <- paste0("hist.", modmeth, ".mod", mymod)
  myplotname <- "hist.test."
  grDevices::png(paste0(imgdir, myplotname, ".png"), width = plotwidth, height = plotheight)
  rewiring_score <- result$T_star
  graphics::hist(main = paste0("True Val = ", signif(result$TS, 3),"\n (p value = " , signif(result$pval,3),")"), outer = FALSE, rewiring_score)
  graphics::abline(v = result$TS, col = "red")
  grDevices::dev.off()
  
  write(paste0("<img src='", htmlinfo$imgstr, myplotname, ".png", "' alt='", myplotname, "' height='", plotheight, "' width='", plotwidth,
               "'><br>\n"), modhtmlfile, append = TRUE)
}

regulatorSummaryAndRank <- function(rankdf, htmlinfo) {
    modhtmlfile <- paste0(htmlinfo$htmldir, htmlinfo$indexpath)

    write(paste0("<table style='width:100%' bgcolor='gray'><tr><td><h1>", "Regulator Summary And Rank", "</h1></td></tr></table><br>\n"),
        modhtmlfile, append = TRUE)
    write(table2html(rankdf), modhtmlfile, append = TRUE)
}