@@ -124,11 +124,14 @@ create_upsetdata <- function(res_enrich, use_ids = FALSE) {

 #' res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)

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

 #' gs_upset(res_enrich,

-#'          n_gs = 10)

+#'   n_gs = 10

+#' )

 #'

-#' gs_upset(res_enrich, res_de = res_de, annotation_obj = anno_df,

-#'          n_gs = 8,

-#'          add_de_direction = TRUE, add_de_gsgenes = TRUE)

+#' gs_upset(res_enrich,

+#'   res_de = res_de, annotation_obj = anno_df,

+#'   n_gs = 8,

+#'   add_de_direction = TRUE, add_de_gsgenes = TRUE

+#' )

 #'

 #' # or using the practical gtl (GeneTonicList)

 #' gtl_macrophage <- GeneTonic_list(

@@ -138,9 +141,11 @@ create_upsetdata <- function(res_enrich, use_ids = FALSE) {

 #'   annotation_obj = anno_df

 #' )

 #'

-#' gs_upset(gtl = gtl_macrophage,

-#'          n_gs = 15,

-#'          add_de_direction = TRUE, add_de_gsgenes = TRUE)

+#' gs_upset(

+#'   gtl = gtl_macrophage,

+#'   n_gs = 15,

+#'   add_de_direction = TRUE, add_de_gsgenes = TRUE

+#' )

 gs_upset <- function(res_enrich,

                      res_de = NULL,

                      annotation_obj = NULL,

@@ -153,7 +158,6 @@ gs_upset <- function(res_enrich,

                      col_downDE = "#377EB8",

                      upset_geom = geom_point(size = 2),

                      return_upsetgsg = FALSE) {

-

   if (!is.null(gtl)) {

     checkup_gtl(gtl)

     # dds <- gtl$dds

@@ -178,36 +182,41 @@ gs_upset <- function(res_enrich,

   upgsg <- create_upsetdata(re)

   if (add_de_direction) {

-    if (is.null(res_de) | is.null(annotation_obj))

+    if (is.null(res_de) | is.null(annotation_obj)) {

       stop("DE results and annotation required if `add_de_direction` is TRUE, please provide them as `res_de` and `annotation_obj`")

+    }

     upgsg$logFC <- res_de[annotation_obj$gene_id[

-      match(rownames(upgsg), annotation_obj$gene_name)], "log2FoldChange"]

+      match(rownames(upgsg), annotation_obj$gene_name)

+    ], "log2FoldChange"]

     upgsg$logFCsign <- upgsg$logFC >= 0

     param_upset_baseanno <- list(

-      'Intersection size' = intersection_size(

+      "Intersection size" = intersection_size(

         counts = FALSE,

         mapping = aes_string(fill = "logFCsign")

       ) +

         scale_fill_manual(

-          values=c('FALSE' = col_downDE, 'TRUE' = col_upDE),

+          values = c("FALSE" = col_downDE, "TRUE" = col_upDE),

           labels = c("logFC<0", "logFC>0"),

-          name = "") +

-        theme(legend.position="bottom")

+          name = ""

+        ) +

+        theme(legend.position = "bottom")

     )

   } else {

     param_upset_baseanno <- "auto"

   }

-  if (add_de_gsgenes){

-    if (is.null(res_de) | is.null(annotation_obj))

+  if (add_de_gsgenes) {

+    if (is.null(res_de) | is.null(annotation_obj)) {

       stop("DE results and annotation required if `add_de_gsgenes` is TRUE, please provide them as `res_de` and `annotation_obj`")

+    }

     upgsg$logFC <- res_de[annotation_obj$gene_id[

-      match(rownames(upgsg), annotation_obj$gene_name)], "log2FoldChange"]

+      match(rownames(upgsg), annotation_obj$gene_name)

+    ], "log2FoldChange"]

     upgsg$logFCsign <- upgsg$logFC >= 0

     param_upset_anno <- list(

-      'logFC' = (

+      "logFC" = (

         ggplot(mapping = aes_string(x = "intersection", y = "logFC")) +

           geom_jitter(aes_string(color = "logFC"), na.rm = TRUE) +

           # geom_violin(alpha = 0.5, na.rm = TRUE) +

@@ -231,12 +240,9 @@ gs_upset <- function(res_enrich,

     name = "gsg upset",

     matrix = intersection_matrix(

       geom = upset_geom

-    ) + scale_y_discrete(position="right"),

+    ) + scale_y_discrete(position = "right"),

     base_annotations = param_upset_baseanno,

     annotations = param_upset_anno,

-    width_ratio=0.1

+    width_ratio = 0.1

   )

-

 }

-

-