@@ -30,7 +30,7 @@ NULL

 #'

 #' Details on how this object has been created are included in the `create_gt_data.R`

 #' script, included in the `scripts` folder of the `GeneTonic` package.

-#' 

+#'

 #' @family pathway-analysis-results

 #'

 #' @references Alasoo, et al. "Shared genetic effects on chromatin and gene

@@ -54,7 +54,7 @@ NULL

 #'

 #' Details on how this object has been created are included in the `create_gt_data.R`

 #' script, included in the `scripts` folder of the `GeneTonic` package.

-#' 

+#'

 #' @family pathway-analysis-results

 #'

 #' @references Alasoo, et al. "Shared genetic effects on chromatin and gene

@@ -79,7 +79,7 @@ NULL

 #'

 #' Details on how this object has been created are included in the `create_gt_data.R`

 #' script, included in the `scripts` folder of the `GeneTonic` package.

-#' 

+#'

 #' @family pathway-analysis-results

 #'

 #' @references Alasoo, et al. "Shared genetic effects on chromatin and gene

@@ -111,6 +111,3 @@ NULL

 #' @name fgseaRes

 #' @docType data

 NULL

-

-

-

@@ -44,7 +44,7 @@

 #'

 #' # dds object

 #' data("gse", package = "macrophage")

-#' dds_macrophage <- DESeqDataSet(gse, design = ~line + condition)

+#' dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)

 #' rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)

 #' dds_macrophage <- estimateSizeFactors(dds_macrophage)

 #'

@@ -52,9 +52,10 @@

 #' anno_df <- data.frame(

 #'   gene_id = rownames(dds_macrophage),

 #'   gene_name = mapIds(org.Hs.eg.db,

-#'                      keys = rownames(dds_macrophage),

-#'                      column = "SYMBOL",

-#'                      keytype = "ENSEMBL"),

+#'     keys = rownames(dds_macrophage),

+#'     column = "SYMBOL",

+#'     keytype = "ENSEMBL"

+#'   ),

 #'   stringsAsFactors = FALSE,

 #'   row.names = rownames(dds_macrophage)

 #' )

@@ -77,22 +78,26 @@

 #' )

 #'

 #' # now everything is in place to launch the app

-#' if (interactive())

+#' if (interactive()) {

 #'   GeneTonic(gtl = gtl_macrophage)

+#' }

 GeneTonic_list <- function(dds,

-                      res_de,

-                      res_enrich,

-                      annotation_obj) {

-

-  checkup_GeneTonic(dds,

-                    res_de,

-                    res_enrich,

-                    annotation_obj)

+                           res_de,

+                           res_enrich,

+                           annotation_obj) {

+  checkup_GeneTonic(

+    dds,

+    res_de,

+    res_enrich,

+    annotation_obj

+  )

-  gtl <- list(dds = dds,

-              res_de = res_de,

-              res_enrich = res_enrich,

-              annotation_obj = annotation_obj)

+  gtl <- list(

+    dds = dds,

+    res_de = res_de,

+    res_enrich = res_enrich,

+    annotation_obj = annotation_obj

+  )

   describe_gtl(gtl)

@@ -111,7 +116,6 @@ GeneTonic_list <- function(dds,

 #' @return Invisible NULL - the information is displayed as a message in the

 #' console

 describe_gtl <- function(gtl) {

-

   dds <- gtl$dds

   res_de <- gtl$res_de

   res_enrich <- gtl$res_enrich

@@ -138,12 +142,15 @@ describe_gtl <- function(gtl) {

   message(

     sprintf(

       "Providing an expression object (as DESeqDataset) of %d features over %d samples",

-      n_features, n_samples)

+      n_features, n_samples

+    )

   )

   message("\n----- res_de object -----")

   message(

-    sprintf("Providing a DE result object (as DESeqResults), %d features tested, %d found as DE",

-            n_tested, n_DE)

+    sprintf(

+      "Providing a DE result object (as DESeqResults), %d features tested, %d found as DE",

+      n_tested, n_DE

+    )

   )

   message(sprintf("Upregulated:     %d", n_upDE))

   message(sprintf("Downregulated:   %d", n_downDE))

@@ -158,7 +165,8 @@ describe_gtl <- function(gtl) {

   message(

     sprintf(

       "Providing an annotation object of %d features with information on %d identifier types",

-      n_featanno, n_featids)

+      n_featanno, n_featids

+    )

   )

   return(invisible(NULL))

@@ -202,7 +210,8 @@ go_2_html <- function(go_id,

       lapply(Synonym(fullinfo), function(arg) {

         paste0(tags$b("Synonym: "), arg, tags$br())

       })

-    ), collapse = ""

+    ),

+    collapse = ""

   )

   go_secondary <- Secondary(fullinfo)

   if (!is.null(res_enrich)) {

@@ -225,9 +234,10 @@ go_2_html <- function(go_id,

     ifelse(

       !is.null(res_enrich),

       paste0(tags$b("p-value: "), go_pvalue, tags$br(),

-             tags$b("Z-score: "), go_zscore, tags$br(),

-             tags$b("Aggregated score: "), go_aggrscore, tags$br(),

-             collapse = ""),

+        tags$b("Z-score: "), go_zscore, tags$br(),

+        tags$b("Aggregated score: "), go_aggrscore, tags$br(),

+        collapse = ""

+      ),

       ""

     ),

     tags$b("Ontology: "), go_ontology, tags$br(), tags$br(),

@@ -236,7 +246,8 @@ go_2_html <- function(go_id,

     ifelse(

       length(go_secondary) > 0,

       paste0(tags$b("Secondary: "), go_secondary, collapse = ""),

-      "")

+      ""

+    )

   )

   return(HTML(mycontent))

 }

@@ -248,10 +259,12 @@ go_2_html <- function(go_id,

 #' @return HTML for an action button

 #' @noRd

 .link2amigo <- function(val) {

-  sprintf('<a href = "http://amigo.geneontology.org/amigo/term/%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',

-          val,

-          .actionbutton_biocstyle,

-          val)

+  sprintf(

+    '<a href = "http://amigo.geneontology.org/amigo/term/%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',

+    val,

+    .actionbutton_biocstyle,

+    val

+  )

 }

 #' Information on a gene

@@ -284,9 +297,11 @@ geneinfo_2_html <- function(gene_id,

   if (!is.null(res_de)) {

     gid <- match(gene_id, res_de$SYMBOL)

     if (is.na(gid)) {

-      message("Could not find the specified gene (`", gene_id,

-              "`) in the `res_de` object. \n",

-              "Still, the general HTML content has been generated.")

+      message(

+        "Could not find the specified gene (`", gene_id,

+        "`) in the `res_de` object. \n",

+        "Still, the general HTML content has been generated."

+      )

       gene_adjpvalue <- tags$em("not found")

       gene_logfc <- tags$em("not found")

     } else {

@@ -303,8 +318,9 @@ geneinfo_2_html <- function(gene_id,

     ifelse(

       !is.null(res_de),

       paste0(tags$b("DE p-value (adjusted): "), gene_adjpvalue, tags$br(),

-             tags$b("DE log2FoldChange: "), gene_logfc,

-             collapse = ""),

+        tags$b("DE log2FoldChange: "), gene_logfc,

+        collapse = ""

+      ),

       ""

     )

   )

@@ -318,10 +334,12 @@ geneinfo_2_html <- function(gene_id,

 #' @return HTML for an action button

 #' @noRd

 .link2ncbi <- function(val) {

-  sprintf('<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',

-          val,

-          .actionbutton_biocstyle,

-          val)

+  sprintf(

+    '<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',

+    val,

+    .actionbutton_biocstyle,

+    val

+  )

 }

 #' Link to the GeneCards database

@@ -331,10 +349,12 @@ geneinfo_2_html <- function(gene_id,

 #' @return HTML for an action button

 #' @noRd

 .link2genecards <- function(val) {

-  sprintf('<a href = "https://www.genecards.org/cgi-bin/carddisp.pl?gene=%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',

-          val,

-          .actionbutton_biocstyle,

-          val)

+  sprintf(

+    '<a href = "https://www.genecards.org/cgi-bin/carddisp.pl?gene=%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',

+    val,

+    .actionbutton_biocstyle,

+    val

+  )

 }

 #' Link to the GTEx Portal

@@ -344,10 +364,12 @@ geneinfo_2_html <- function(gene_id,

 #' @return HTML for an action button

 #' @noRd

 .link2gtex <- function(val) {

-  sprintf('<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-dna"></i>%s</a>',

-          val,

-          .actionbutton_biocstyle,

-          val)

+  sprintf(

+    '<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s"><i class="fa fa-dna"></i>%s</a>',

+    val,

+    .actionbutton_biocstyle,

+    val

+  )

 }

@@ -365,19 +387,23 @@ generate_buttons_hubgenes <- function(x) {

       '<a href = "http://www.ncbi.nlm.nih.gov/gene/?term=%s[sym]" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',

       x,

       .actionbutton_biocstyle,

-      "NCBI"),

+      "NCBI"

+    ),

     sprintf(

       '<a href = "https://www.genecards.org/cgi-bin/carddisp.pl?gene=%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',

       x,

       .actionbutton_biocstyle,

-      "GeneCards"),

+      "GeneCards"

+    ),

     sprintf(

       '<a href = "https://www.gtexportal.org/home/gene/%s" target = "_blank" class = "btn btn-primary" style = "%s">%s</a>',

       x,

       .actionbutton_biocstyle,

-      "GTEx"),

-    tags$br(style="display:inline-block"),

-    collapse = "\t")

+      "GTEx"

+    ),

+    tags$br(style = "display:inline-block"),

+    collapse = "\t"

+  )

   return(mybuttons)

 }

@@ -399,7 +425,7 @@ generate_buttons_hubgenes <- function(x) {

 #' @examples

 #' a <- seq(1, 21, 2)

 #' b <- seq(1, 11, 2)

-#' overlap_coefficient(a,b)

+#' overlap_coefficient(a, b)

 overlap_coefficient <- function(x, y) {

   length(intersect(x, y)) / min(length(x), length(y))

 }

@@ -417,7 +443,7 @@ overlap_coefficient <- function(x, y) {

 #' @examples

 #' a <- seq(1, 21, 2)

 #' b <- seq(1, 11, 2)

-#' overlap_jaccard_index(a,b)

+#' overlap_jaccard_index(a, b)

 overlap_jaccard_index <- function(x, y) {

   length(intersect(x, y)) / length(unique(c(x, y)))

   # about 2x faster than using union()

@@ -463,20 +489,22 @@ overlap_jaccard_index <- function(x, y) {

 #' res_df <- deseqresult2df(res_macrophage_IFNg_vs_naive)

 #' library("magrittr")

 #' library("DT")

-#' DT::datatable(res_df [1:50, ],

-#'               options = list(

-#'                 pageLength = 25,

-#'                 columnDefs = list(

-#'                   list(className = "dt-center", targets = "_all")

-#'                 )

-#'               )

+#' DT::datatable(res_df[1:50, ],

+#'   options = list(

+#'     pageLength = 25,

+#'     columnDefs = list(

+#'       list(className = "dt-center", targets = "_all")

+#'     )

+#'   )

 #' ) %>%

 #'   formatRound(columns = c("log2FoldChange"), digits = 3) %>%

 #'   formatStyle(

 #'     "log2FoldChange",

-#'     background = styleColorBar_divergent(res_df$log2FoldChange,

-#'                                          scales::alpha("navyblue", 0.4),

-#'                                          scales::alpha("darkred", 0.4)),

+#'     background = styleColorBar_divergent(

+#'       res_df$log2FoldChange,

+#'       scales::alpha("navyblue", 0.4),

+#'       scales::alpha("darkred", 0.4)

+#'     ),

 #'     backgroundSize = "100% 90%",

 #'     backgroundRepeat = "no-repeat",

 #'     backgroundPosition = "center"

@@ -484,17 +512,19 @@ overlap_jaccard_index <- function(x, y) {

 #'

 #'

 #' simplest_df <- data.frame(

-#'   a = c(rep("a",9)),

+#'   a = c(rep("a", 9)),

 #'   value = c(-4, -3, -2, -1, 0, 1, 2, 3, 4)

 #' )

 #'

 #' # or with a very simple data frame

 #' DT::datatable(simplest_df) %>%

 #'   formatStyle(

-#'     'value',

-#'     background = styleColorBar_divergent(simplest_df$value,

-#'                                          scales::alpha("forestgreen", 0.4),

-#'                                          scales::alpha("gold", 0.4)),

+#'     "value",

+#'     background = styleColorBar_divergent(

+#'       simplest_df$value,

+#'       scales::alpha("forestgreen", 0.4),

+#'       scales::alpha("gold", 0.4)

+#'     ),

 #'     backgroundSize = "100% 90%",

 #'     backgroundRepeat = "no-repeat",

 #'     backgroundPosition = "center"

@@ -502,12 +532,13 @@ overlap_jaccard_index <- function(x, y) {

 styleColorBar_divergent <- function(data,

                                     color_pos,

                                     color_neg) {

-

   max_val <- max(abs(data))

   JS(

     sprintf(

       "isNaN(parseFloat(value)) || value < 0 ? 'linear-gradient(90deg, transparent, transparent ' + (50 + value/%s * 50) + '%%, %s ' + (50 + value/%s * 50) + '%%,%s  50%%,transparent 50%%)': 'linear-gradient(90deg, transparent, transparent 50%%, %s 50%%, %s ' + (50 + value/%s * 50) + '%%, transparent ' + (50 + value/%s * 50) + '%%)'",

-      max_val, color_pos, max_val, color_pos, color_neg, color_neg, max_val, max_val))

+      max_val, color_pos, max_val, color_pos, color_neg, color_neg, max_val, max_val

+    )

+  )

 }

@@ -530,21 +561,25 @@ styleColorBar_divergent <- function(data,

 #'

 #' @examples

 #' a <- 1:9

-#' pal <- RColorBrewer::brewer.pal(9,"Set1")

+#' pal <- RColorBrewer::brewer.pal(9, "Set1")

 #' map2color(a, pal)

 #' plot(a, col = map2color(a, pal), pch = 20, cex = 4)

 #'

 #' b <- 1:50

 #' pal2 <- grDevices::colorRampPalette(

-#'   RColorBrewer::brewer.pal(name = "RdYlBu", 11))(50)

+#'   RColorBrewer::brewer.pal(name = "RdYlBu", 11)

+#' )(50)

 #' plot(b, col = map2color(b, pal2), pch = 20, cex = 3)

 map2color <- function(x, pal, limits = NULL) {

-  if (is.null(limits))

+  if (is.null(limits)) {

     limits <- range(x)

+  }

   pal[findInterval(x, seq(limits[1],

-                          limits[2],

-                          length.out = length(pal) + 1),

-                   all.inside = TRUE)]

+    limits[2],

+    length.out = length(pal) + 1

+  ),

+  all.inside = TRUE

+  )]

 }

@@ -566,14 +601,17 @@ map2color <- function(x, pal, limits = NULL) {

 #' check_colors(mypal)

 #' mypal2 <- rev(

 #'   scales::alpha(

-#'     colorRampPalette(RColorBrewer::brewer.pal(name = "RdYlBu", 11))(50), 0.4))

+#'     colorRampPalette(RColorBrewer::brewer.pal(name = "RdYlBu", 11))(50), 0.4

+#'   )

+#' )

 #' check_colors(mypal2)

 #' # useful with long vectors to check at once if all cols are fine

 #' all(check_colors(mypal2))

 check_colors <- function(x) {

   vapply(x, function(col) {

     tryCatch(is.matrix(col2rgb(col)),

-             error = function(e) FALSE)

+      error = function(e) FALSE

+    )

   }, logical(1))

 }

@@ -598,15 +636,17 @@ check_colors <- function(x) {

 #' res_df <- deseqresult2df(res_macrophage_IFNg_vs_naive)

 #' head(res_df)

 deseqresult2df <- function(res_de, FDR = NULL) {

-  if (!is(res_de, "DESeqResults"))

+  if (!is(res_de, "DESeqResults")) {

     stop("Not a DESeqResults object.")

+  }

   res <- as.data.frame(res_de)

   res <- cbind(rownames(res), res)

   names(res)[1] <- "id"

   res$id <- as.character(res$id)

   res <- res[order(res$padj), ]

-  if (!is.null(FDR))

+  if (!is.null(FDR)) {

     res <- res[!(is.na(res$padj)) & res$padj <= FDR, ]

+  }

   res

 }

@@ -627,10 +667,9 @@ deseqresult2df <- function(res_de, FDR = NULL) {

 #' @examples

 #' library("igraph")

 #' g <- make_full_graph(5) %du% make_full_graph(5) %du% make_full_graph(5)

-#' g <- add_edges(g, c(1,6, 1,11, 6, 11))

+#' g <- add_edges(g, c(1, 6, 1, 11, 6, 11))

 #' export_to_sif(g, tempfile())

 export_to_sif <- function(g, sif_file = "", edge_label = "relates_to") {

-

   stopifnot(is(g, "igraph"))

   stopifnot(is.character(sif_file) & length(sif_file) == 1)

   sif_file <- normalizePath(sif_file, mustWork = FALSE)

@@ -643,8 +682,10 @@ export_to_sif <- function(g, sif_file = "", edge_label = "relates_to") {

     n2 = el[, 2]

   )

   message("Saving the file to ", sif_file)

-  write.table(sif_df, file = sif_file, sep = "\t", quote = FALSE,

-              col.names = FALSE, row.names = FALSE)

+  write.table(sif_df,

+    file = sif_file, sep = "\t", quote = FALSE,

+    col.names = FALSE, row.names = FALSE

+  )

   message("Done!")

   return(invisible(sif_file))

 }

@@ -677,9 +718,9 @@ GeneTonic_footer <- fluidRow(

 .onLoad <- function(libname, pkgname) {

   # Create link to logo

-  #nocov start

+  # nocov start

   shiny::addResourcePath("GeneTonic", system.file("www", package = "GeneTonic"))

-  #nocov end

+  # nocov end

 }

@@ -694,13 +735,15 @@ gt_downloadButton <- function(outputId,

                               icon = "magic",

                               class = NULL,

                               ...) {

-  aTag <- tags$a(id = outputId,

-                 class = paste("btn btn-default shiny-download-link", class),

-                 href = "",

-                 target = "_blank",

-                 download = NA,

-                 icon(icon),

-                 label)

+  aTag <- tags$a(

+    id = outputId,

+    class = paste("btn btn-default shiny-download-link", class),

+    href = "",

+    target = "_blank",

+    download = NA,

+    icon(icon),

+    label

+  )

 }

@@ -2,16 +2,16 @@

 #'

 #' `GeneTonic` is a Bioconductor package that provides an interactive Shiny-based

 #' graphical user interface for streamlining the interpretation of RNA-seq data

-#'  

-#' `GeneTonic` simplifies and optimizes the integration of all components of 

-#' Diffeential Expression analysis, with functional enrichment analyis and the 

+#'

+#' `GeneTonic` simplifies and optimizes the integration of all components of

+#' Diffeential Expression analysis, with functional enrichment analyis and the

 #' original expression quantifications.

-#' It does so in a way that makes it easier to generate insightful observations 

-#' and hypothesis - combining the benefits of interactivity and reproducibility, 

-#' e.g. by capturing the features and gene sets of interest highlighted during 

-#' the live session, and creating an HTML report as an artifact where text, 

+#' It does so in a way that makes it easier to generate insightful observations

+#' and hypothesis - combining the benefits of interactivity and reproducibility,

+#' e.g. by capturing the features and gene sets of interest highlighted during

+#' the live session, and creating an HTML report as an artifact where text,

 #' code, and output coexist.

-#'  

+#'

 #' @author Federico Marini \email{marinif@@uni-mainz.de}

 #'

 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term

@@ -61,7 +61,7 @@

 #' @importFrom tidyr separate_rows pivot_longer

 #' @importFrom tools file_ext file_path_sans_ext

 #' @importFrom utils read.delim sessionInfo browseURL citation data write.table

-#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput 

+#' @importFrom visNetwork renderVisNetwork visExport visIgraph visNetworkOutput

 #' visOptions

 #' @importFrom viridis viridis

 #'

@@ -43,7 +43,7 @@

 #'

 #' # dds object

 #' data("gse", package = "macrophage")

-#' dds_macrophage <- DESeqDataSet(gse, design = ~line + condition)

+#' dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)

 #' rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)

 #' dds_macrophage <- estimateSizeFactors(dds_macrophage)

 #'

@@ -51,9 +51,10 @@

 #' anno_df <- data.frame(

 #'   gene_id = rownames(dds_macrophage),

 #'   gene_name = mapIds(org.Hs.eg.db,

-#'                      keys = rownames(dds_macrophage),

-#'                      column = "SYMBOL",

-#'                      keytype = "ENSEMBL"),

+#'     keys = rownames(dds_macrophage),

+#'     column = "SYMBOL",

+#'     keytype = "ENSEMBL"

+#'   ),

 #'   stringsAsFactors = FALSE,

 #'   row.names = rownames(dds_macrophage)

 #' )

@@ -69,17 +70,22 @@

 #' res_enrich <- get_aggrscores(res_enrich, res_de, anno_df)

 #'

 #' # now everything is in place to launch the app

-#' if (interactive())

-#'   GeneTonic(dds = dds_macrophage,

-#'             res_de = res_de,

-#'             res_enrich = res_enrich,

-#'             annotation_obj = anno_df,

-#'             project_id = "myexample")

+#' if (interactive()) {

+#'   GeneTonic(

+#'     dds = dds_macrophage,

+#'     res_de = res_de,

+#'     res_enrich = res_enrich,

+#'     annotation_obj = anno_df,

+#'     project_id = "myexample"

+#'   )

+#' }

 #' # alternatively...

-#' gtl_macrophage <- GeneTonic_list(dds = dds_macrophage,

-#'                                  res_de = res_de,

-#'                                  res_enrich = res_enrich,

-#'                                  annotation_obj = anno_df)

+#' gtl_macrophage <- GeneTonic_list(

+#'   dds = dds_macrophage,

+#'   res_de = res_de,

+#'   res_enrich = res_enrich,

+#'   annotation_obj = anno_df

+#' )

 #' # GeneTonic(gtl = gtl_macrophage)

 GeneTonic <- function(dds,

                       res_de,

@@ -105,15 +111,19 @@ GeneTonic <- function(dds,

   }

   # checks on the objects provided

-  checkup_GeneTonic(dds,

-                    res_de,

-                    res_enrich,

-                    annotation_obj)

+  checkup_GeneTonic(

+    dds,

+    res_de,

+    res_enrich,

+    annotation_obj

+  )

   # clean up the result object, e.g. removing the NAs in the relevant columns

   removed_genes <- is.na(res_de$log2FoldChange)

-  message("Removing ", sum(removed_genes),

-          "/", nrow(res_de), " rows from the DE `res_de` object - log2FC values detected as NA")

+  message(

+    "Removing ", sum(removed_genes),

+    "/", nrow(res_de), " rows from the DE `res_de` object - log2FC values detected as NA"

+  )

   res_de <- res_de[!removed_genes, ]

   # UI definition -----------------------------------------------------------

@@ -128,8 +138,10 @@ GeneTonic <- function(dds,

       # older leftUi elements

       tagList(

         tags$code(tags$h3("GeneTonic")),

-        actionButton("bookmarker", label = "Bookmark", icon = icon("heart"),

-                     style = "color: #ffffff; background-color: #ac0000; border-color: #ffffff", class = "ml-5")

+        actionButton("bookmarker",

+          label = "Bookmark", icon = icon("heart"),

+          style = "color: #ffffff; background-color: #ac0000; border-color: #ffffff", class = "ml-5"

+        )

       ),

       # older rightUi elements

       # ideally to be spaced on the full right side...

@@ -150,8 +162,9 @@ GeneTonic <- function(dds,

             icon = icon("book-open"),

             label = "Open GeneTonic Vignette", style = .actionbutton_biocstyle,

             onclick = ifelse(system.file("doc", "GeneTonic_manual.html", package = "GeneTonic") != "",

-                             "",

-                             "window.open('https://federicomarini.github.io/GeneTonic/articles/GeneTonic_manual.html', '_blank')")

+              "",

+              "window.open('https://federicomarini.github.io/GeneTonic/articles/GeneTonic_manual.html', '_blank')"

+            )

             # sprintf("window.open('http://bioconductor.org/packages/%s/bioc/vignettes/GeneTonic/inst/doc/GeneTonic_manual.html', '_blank')",

             #         ifelse(unlist(packageVersion("GeneTonic"))[2] %% 2L==0L, "release", "devel")

             # )

@@ -187,7 +200,7 @@ GeneTonic <- function(dds,

       ),

       title = bs4Dash::bs4DashBrand(

         title = HTML("<small>GeneTonic</small>"),

-        href =  "https://bioconductor.org/packages/GeneTonic",

+        href = "https://bioconductor.org/packages/GeneTonic",

         # color = "info",

         image = "GeneTonic/GeneTonic.png"

       ),

@@ -195,9 +208,9 @@ GeneTonic <- function(dds,

       status = "gray-dark",

       border = FALSE,

       controlbarIcon = icon("gears"),

-      fixed = TRUE #,

-      # leftUi = 

-      # rightUi = 

+      fixed = TRUE # ,

+      # leftUi =

+      # rightUi =

     ),

     # sidebar definition ------------------------------------------------------

@@ -212,7 +225,6 @@ GeneTonic <- function(dds,

       # src = "logos/online-learning.png",

       elevation = 1,

       opacity = 0.8,

-

       bs4SidebarMenu(

         id = "gt_tabs",

         bs4SidebarMenuItem(

@@ -272,13 +284,11 @@ GeneTonic <- function(dds,

           )

         )

       ),

-

       tags$head(

         tags$style(

           ".biocdlbutton{background-color:#0092AC;} .biocdlbutton{color: #ffffff;}"

         )

       ),

-

       tags$script(HTML("$(function(){

       $(document).keyup(function(e) {

       if (e.which == 17) {

@@ -307,7 +317,8 @@ GeneTonic <- function(dds,

             column(

               width = 1,

               actionButton(

-                "tour_firststeps", label = "", icon = icon("question-circle"),

+                "tour_firststeps",

+                label = "", icon = icon("question-circle"),

                 style = .helpbutton_biocstyle

               )

             )

@@ -374,7 +385,8 @@ GeneTonic <- function(dds,

             column(

               width = 1,

               actionButton(

-                "tour_ggs", label = "", icon = icon("question-circle"),

+                "tour_ggs",

+                label = "", icon = icon("question-circle"),

                 style = .helpbutton_biocstyle

               )

             )

@@ -384,8 +396,9 @@ GeneTonic <- function(dds,

               width = 8,

               withSpinner(

                 visNetworkOutput("ggsnetwork",

-                                 height = "700px",

-                                 width = "100%")

+                  height = "700px",

+                  width = "100%"

+                )

               )

             ),

             column(

@@ -406,7 +419,6 @@ GeneTonic <- function(dds,

               )

             )

           ),

-

           fluidRow(

             bs4Dash::bs4Card(

               width = 12,

@@ -421,11 +433,13 @@ GeneTonic <- function(dds,

                 column(

                   width = 8,

                   uiOutput("ui_backbone_launch"),

-                  radioButtons(inputId = "backbone_on",

-                               label = "Compute the backbone on",

-                               choices = c("genesets", "features"),

-                               selected = "genesets",

-                               inline = TRUE),

+                  radioButtons(

+                    inputId = "backbone_on",

+                    label = "Compute the backbone on",

+                    choices = c("genesets", "features"),

+                    selected = "genesets",

+                    inline = TRUE

+                  ),

                   withSpinner(

                     visNetworkOutput("backbone_graph")

                   )

@@ -437,7 +451,6 @@ GeneTonic <- function(dds,

               )

             )

           )

-

         ),

         # ui panel enrichment map -------------------------------------------------

@@ -450,7 +463,8 @@ GeneTonic <- function(dds,

             column(

               width = 1,

               actionButton(

-                "tour_emap", label = "", icon = icon("question-circle"),

+                "tour_emap",

+                label = "", icon = icon("question-circle"),

                 style = .helpbutton_biocstyle

               )

             )

@@ -464,10 +478,12 @@ GeneTonic <- function(dds,

                     inputId = "emap_colorby",

                     label = "Color emap by",

                     choices = colnames(res_enrich)[unlist(lapply(res_enrich, is.numeric))],

-                    selected = "gs_pvalue"),

+                    selected = "gs_pvalue"

+                  ),

                   visNetworkOutput("emap_visnet",

-                                   height = "700px",

-                                   width = "100%")

+                    height = "700px",

+                    width = "100%"

+                  )

                 )

               )

             ),

@@ -497,7 +513,6 @@ GeneTonic <- function(dds,

                   withSpinner(

                     DT::dataTableOutput("dt_distill")

                   ),

-

                   uiOutput("distill_launch"),

                   numericInput(

                     inputId = "n_genesets_distill",

@@ -529,12 +544,12 @@ GeneTonic <- function(dds,

             column(

               width = 1,

               actionButton(

-                "tour_overview", label = "", icon = icon("question-circle"),

+                "tour_overview",

+                label = "", icon = icon("question-circle"),

                 style = .helpbutton_biocstyle

               )

             )

           ),

-

           fluidRow(

             bs4Dash::column(

               width = 11,

@@ -555,25 +570,31 @@ GeneTonic <- function(dds,

                   tabPanel(

                     title = "Geneset Volcano",

                     withSpinner(plotOutput("gs_volcano",

-                                           height = "650px"))

+                      height = "650px"

+                    ))

                   ),

                   shiny::tabPanel(

                     title = "Geneset Volcano - simplified",

-                    numericInput(inputId = "gs_overlap",

-                                 label = "Gene Set overlap",

-                                 value = 0.6, min = 0, max = 1, step = 0.05),

+                    numericInput(

+                      inputId = "gs_overlap",

+                      label = "Gene Set overlap",

+                      value = 0.6, min = 0, max = 1, step = 0.05

+                    ),

                     withSpinner(plotOutput("gs_volcano_simplified",

-                                           height = "650px"))

+                      height = "650px"

+                    ))

                   ),

                   shiny::tabPanel(

                     title = "Enhanced Table",

                     withSpinner(plotOutput("enriched_funcres",

-                                           height = "650px"))

+                      height = "650px"

+                    ))

                   ),

                   shiny::tabPanel(

                     title = "Enhanced Table - interactive",

                     withSpinner(plotlyOutput("enriched_funcres_plotly",

-                                             height = "650px"))

+                      height = "650px"

+                    ))

                   )

                 )

               )

@@ -591,12 +612,12 @@ GeneTonic <- function(dds,

             column(

               width = 1,

               actionButton(

-                "tour_gsviz", label = "", icon = icon("question-circle"),

+                "tour_gsviz",

+                label = "", icon = icon("question-circle"),