@@ -41,6 +41,7 @@ Imports:

     ggforce,

     ggplot2,

     ggrepel,

+    ggridges,

     GO.db,

     graphics,

     grDevices,

@@ -81,7 +82,7 @@ Encoding: UTF-8

 VignetteBuilder: knitr

 URL: https://github.com/federicomarini/GeneTonic

 BugReports: https://github.com/federicomarini/GeneTonic/issues

-RoxygenNote: 7.2.1

+RoxygenNote: 7.2.3

 Roxygen: list(markdown = TRUE)

 biocViews:

     GUI, GeneExpression, Software, Transcription, Transcriptomics, Visualization,

@@ -124,6 +124,8 @@ importFrom(expm,"%^%")

 importFrom(ggforce,geom_sina)

 importFrom(ggrepel,geom_label_repel)

 importFrom(ggrepel,geom_text_repel)

+importFrom(ggridges,geom_density_ridges)

+importFrom(ggridges,position_points_jitter)

 importFrom(grDevices,col2rgb)

 importFrom(grDevices,colorRampPalette)

 importFrom(grDevices,rgb)

@@ -37,6 +37,7 @@

 #' @importFrom ggforce geom_sina

 #' @import ggplot2

 #' @importFrom ggrepel geom_label_repel geom_text_repel

+#' @importFrom ggridges geom_density_ridges position_points_jitter

 #' @import GO.db

 #' @importFrom graphics par plot

 #' @importFrom grDevices colorRampPalette rgb col2rgb

@@ -19,9 +19,14 @@

 #' available in `res_enrich`. Lists the gene sets to be displayed.

 #' @param chars_limit Integer, number of characters to be displayed for each

 #' geneset name.

+#' @param plot_style Character value, one of "point" or "ridgeline". Defines the 

+#' style of the plot to summarize visually the table.

+#' @param ridge_color Character value, one of "gs_id" or "gs_score", controls the

+#' fill color of the ridge lines. If selecting "gs_score", the `z_score` column

+#' must be present in the enrichment results table - see `get_aggrscores()` to do

+#' that.

 #' @param plot_title Character string, used as title for the plot. If left `NULL`,

-#' it defaults to a general description of the plot and of the DE contrast

-#'

+#' it defaults to a general description of the plot and of the DE contrast.

 #'

 #' @return A `ggplot` object

 #' @export

@@ -64,6 +69,20 @@

 #'   anno_df,

 #'   n_gs = 10

 #' )

+#' 

+#' # using the ridge line as a style, also coloring by the Z score

+#' res_enrich_withscores <- get_aggrscores(

+#'   res_enrich,

+#'   res_de,

+#'   anno_df

+#' )

+#' enhance_table(res_enrich_withscores,

+#'   res_de,

+#'   anno_df,

+#'   n_gs = 10, 

+#'   plot_style = "ridgeline",

+#'   ridge_color = "gs_score"

+#' )

 enhance_table <- function(res_enrich,

                           res_de,

                           annotation_obj,

@@ -71,6 +90,8 @@ enhance_table <- function(res_enrich,

                           n_gs = 50,

                           gs_ids = NULL,

                           chars_limit = 70,

+                          plot_style = c("point", "ridgeline"),

+                          ridge_color = c("gs_id", "gs_score"),

                           plot_title = NULL) {

   if (!is.null(gtl)) {

     checkup_gtl(gtl)

@@ -79,7 +100,10 @@ enhance_table <- function(res_enrich,

     res_enrich <- gtl$res_enrich

     annotation_obj <- gtl$annotation_obj

   }

-

+  

+  plot_style <- match.arg(plot_style, c("point", "ridgeline"))

+  ridge_color <- match.arg(ridge_color, c("gs_id", "gs_score"))

+  

   n_gs <- min(n_gs, nrow(res_enrich))

   gs_to_use <- unique(

@@ -128,27 +152,89 @@ enhance_table <- function(res_enrich,

   gs_fulllist$gs_desc <- factor(gs_fulllist$gs_desc, levels = rev(levels(gs_fulllist$gs_desc)))

   max_lfc <- max(abs(range(gs_fulllist$log2FoldChange)))

-  p <- ggplot(

-    gs_fulllist, aes_string(

-      x = "log2FoldChange",

-      y = "gs_desc",

-      fill = "gs_id",

-      text = "gene_name"

-    )

-  ) +

-    scale_x_continuous(limits = c(-max_lfc, max_lfc)) +

-    geom_point(alpha = 0.7, shape = 21, size = 2) +

-    theme_minimal() +

-    geom_vline(aes(xintercept = 0), col = "steelblue", alpha = 0.4) +

-    theme(legend.position = "none") +

-    scale_y_discrete(

-      name = "",

-      labels = paste0(

-        substr(as.character(unique(gs_fulllist$gs_desc)), 1, chars_limit),

-        " | ", unique(gs_fulllist$gs_id)

+  # common elements here

+  gs_labels <- paste0(

+    substr(as.character(unique(gs_fulllist$gs_desc)), 1, chars_limit),

+    " | ", unique(gs_fulllist$gs_id)

+  )

+  

+  if (plot_style == "point") {

+    p <- ggplot(

+      gs_fulllist, aes_string(

+        x = "log2FoldChange",

+        y = "gs_desc",

+        fill = "gs_id",

+        text = "gene_name"

       )

     ) +

-    labs(x = "log2 Fold Change")

+      scale_x_continuous(limits = c(-max_lfc, max_lfc)) +

+      geom_point(alpha = 0.7, shape = 21, size = 2) +

+      theme_minimal() +

+      geom_vline(aes(xintercept = 0), col = "steelblue", alpha = 0.4) +

+      theme(legend.position = "none") +

+      scale_y_discrete(

+        name = "",

+        labels = gs_labels

+      ) +

+      labs(x = "log2 Fold Change")

+    

+  } else if (plot_style == "ridgeline") {

+    

+    if (ridge_color == "gs_score" & is.null(res_enrich$z_score)) {

+      message("Fallback to plotting the ridgelines according to geneset id (Z score required)")

+      ridge_color <- "gs_id"

+    }  

+    

+    if (ridge_color == "gs_score") {

+      gs_fulllist$gs_zscore <- res_enrich$z_score[match(gs_fulllist$gs_id, res_enrich$gs_id)]

+      p <- ggplot(

+        gs_fulllist, aes_string(

+          x = "log2FoldChange",

+          y = "gs_desc",

+          fill = "gs_zscore"

+        )

+      ) +

+        scale_x_continuous(limits = c(-max_lfc, max_lfc)) + 

+        scale_fill_gradient2(low = "#313695", mid = "#FFFFE5", high = "#A50026") + 

+        ggridges::geom_density_ridges(

+          aes_string(group = "gs_id"),

+          point_color = "#00000066",

+          jittered_points = TRUE, scale = .95, rel_min_height = .01,

+          point_shape = "|", point_size = 3, size = 0.25,

+          position = ggridges::position_points_jitter(height = 0)) +

+        theme_minimal() +

+        geom_vline(aes(xintercept = 0), col = "steelblue", alpha = 0.4) +

+        scale_y_discrete(

+          name = "",

+          labels = gs_labels

+        ) +

+        labs(x = "log2 Fold Change")

+    }

+    else if (ridge_color == "gs_id") {

+      p <- ggplot(

+        gs_fulllist, aes_string(

+          x = "log2FoldChange",

+          y = "gs_desc",

+          fill = "gs_id"

+        )

+      ) +

+        scale_x_continuous(limits = c(-max_lfc, max_lfc)) + 

+        ggridges::geom_density_ridges(

+          aes_string(group = "gs_id"),

+          point_color = "#00000066",

+          jittered_points = TRUE, scale = .95, rel_min_height = .01,

+          point_shape = "|", point_size = 3, size = 0.25,

+          position = ggridges::position_points_jitter(height = 0)) +

+        theme_minimal() +

+        geom_vline(aes(xintercept = 0), col = "steelblue", alpha = 0.4) +

+        theme(legend.position = "none") +

+        scale_y_discrete(

+          name = "",

+          labels = gs_labels

+        ) +

+        labs(x = "log2 Fold Change")

+    }

+  }

   if (is.null(plot_title)) {

     p <- p + ggtitle(paste0("Enrichment overview - ", this_contrast))

@@ -223,7 +223,7 @@ gs_fuzzyclustering <- function(res_enrich,

     group_by(.data$gs_fuzzycluster) %>%

     arrange(.data$gs_pvalue) %>%

     slice(1) %>%

-    select(.data$gs_id, .data$gs_fuzzycluster)

+    select("gs_id", "gs_fuzzycluster")

   # handling this with tuple to account where the gene set is most representative

   gs_mostsig_tuple <- paste0(gs_mostsig$gs_id, "|", gs_mostsig$gs_fuzzycluster)

@@ -519,7 +519,7 @@ gs_horizon <- function(res_enrich,

       mutate(gs_description = factor(.data$gs_description, rev(unique(.data$gs_description)))) %>%

       arrange((.data$logp10)) %>%

       ggplot(aes_string(x = "gs_description", y = "logp10")) +

-      geom_line(aes_string(group = "scenario", col = "scenario"), size = 3, alpha = 0.7) +

+      geom_line(aes_string(group = "scenario", col = "scenario"), linewidth = 3, alpha = 0.7) +

       geom_point(aes_string(fill = "z_score"), size = 4, pch = 21) +

       scale_color_brewer(palette = "Set2") +

       scale_fill_gradient2(low = "#313695", mid = "#FFFFE5", high = "#A50026") +

@@ -542,7 +542,7 @@ gs_horizon <- function(res_enrich,

       mutate(gs_description = factor(.data$gs_description, rev(unique(nicerorder_terms)))) %>%

       arrange(desc(.data$logp10)) %>%

       ggplot(aes_string(x = "gs_description", y = "logp10")) +

-      geom_line(aes_string(group = "scenario", col = "scenario"), size = 3, alpha = 0.7) +

+      geom_line(aes_string(group = "scenario", col = "scenario"), linewidth = 3, alpha = 0.7) +

       scale_color_brewer(palette = "Set2") +

       geom_point(aes_string(fill = "z_score"), size = 4, pch = 21) +

       scale_fill_gradient2(low = "#313695", mid = "#FFFFE5", high = "#A50026") +

@@ -12,6 +12,8 @@ enhance_table(

   n_gs = 50,

   gs_ids = NULL,

   chars_limit = 70,

+  plot_style = c("point", "ridgeline"),

+  ridge_color = c("gs_id", "gs_score"),

   plot_title = NULL

 )

 }

@@ -38,8 +40,16 @@ available in \code{res_enrich}. Lists the gene sets to be displayed.}

 \item{chars_limit}{Integer, number of characters to be displayed for each

 geneset name.}

+\item{plot_style}{Character value, one of "point" or "ridgeline". Defines the

+style of the plot to summarize visually the table.}

+

+\item{ridge_color}{Character value, one of "gs_id" or "gs_score", controls the

+fill color of the ridge lines. If selecting "gs_score", the \code{z_score} column

+must be present in the enrichment results table - see \code{get_aggrscores()} to do

+that.}

+

 \item{plot_title}{Character string, used as title for the plot. If left \code{NULL},

-it defaults to a general description of the plot and of the DE contrast}

+it defaults to a general description of the plot and of the DE contrast.}

 }

 \value{

 A \code{ggplot} object

@@ -87,4 +97,18 @@ enhance_table(res_enrich,

   anno_df,

   n_gs = 10

 )

+

+# using the ridge line as a style, also coloring by the Z score

+res_enrich_withscores <- get_aggrscores(

+  res_enrich,

+  res_de,

+  anno_df

+)

+enhance_table(res_enrich_withscores,

+  res_de,

+  anno_df,

+  n_gs = 10, 

+  plot_style = "ridgeline",

+  ridge_color = "gs_score"

+)

 }

@@ -37,6 +37,32 @@ test_that("Enhanced table is created", {

   )

   expect_is(p2, "gg")

+  p_ridge <- enhance_table(with_scores,

+    res_macrophage_IFNg_vs_naive,

+    annotation_obj = anno_df,

+    n_gs = 5,

+    plot_style = "ridgeline"

+  )

+  expect_is(p_ridge, "gg")

+  

+  p_ridge_zscorecol <- enhance_table(with_scores,

+    res_macrophage_IFNg_vs_naive,

+    annotation_obj = anno_df,

+    n_gs = 5,

+    plot_style = "ridgeline",

+    ridge_color = "gs_score"

+  )

+  expect_is(p_ridge_zscorecol, "gg")

+  

+  expect_message({

+    p_ridge_fallback <- enhance_table(

+      gtl = gtl_macrophage,

+      n_gs = 5,

+      plot_style = "ridgeline",

+      ridge_color = "gs_score")

+  })

+  

+  

   re_modified <- res_enrich_IFNg_vs_naive

   # patching up some letters to mess up the name of a gene

   re_modified$gs_genes[1] <- 

@@ -24,6 +24,14 @@ test_that("Gene set dendrogram is created", {

   expect_is(my_dend2, "dendrogram")

   expect_is(my_dend3, "dendrogram")

   expect_is(my_dend4, "dendrogram")

+  

+  my_dend_pval <- gs_dendro(res_enrich_withscores, n_gs = 20,

+                            color_leaves_by = "gs_pvalue")

+  expect_is(my_dend_pval, "dendrogram")

+  

+  re_subset <- res_enrich_withscores[res_enrich_withscores[1:12, ]$z_score >= 0, ]

+  my_dend_subset <- gs_dendro(re_subset, n_gs = 12, color_leaves_by = "z_score")

+  expect_is(my_dend_subset, "dendrogram")

   expect_warning(gs_dendro(res_enrich_withscores,

     n_gs = 5,