diff --git a/R/server.R b/R/server.R index 00600c3..18cd5d4 100644 --- a/R/server.R +++ b/R/server.R @@ -159,6 +159,8 @@ server <- function(input, output, session) { DT::formatRound("p_value", digits = 4) |> DT::formatPercentage(c("total_ratio", "query_ratio"), digits = 1) }) + + output$gsea_plot_ranking <- plotly::renderPlotly(gsea_plot_ranking) } #' Create a displayable data table from the gene results data. diff --git a/R/sysdata.rda b/R/sysdata.rda new file mode 100644 index 0000000..c785d0c Binary files /dev/null and b/R/sysdata.rda differ diff --git a/R/ui.R b/R/ui.R index 9040149..b7e071f 100644 --- a/R/ui.R +++ b/R/ui.R @@ -141,10 +141,33 @@ ui <- function() { ) ), tabPanel( - title = "Help" - ), - tabPanel( - title = "Publication" + title = "Additional information", + div( + class = "container", + h2("Number of interesting genes along the ranking"), + p(HTML(paste0( + "The notion of ubiquitous genes or housekeeping genes implies ", + "some kind of enrichment of important genes. Within groups of ", + "genes with certain biological associations, these genes should ", + "be overrepresented. We use GeneOntology terms as well as some ", + "other gene set sources to represent this concept. The following ", + "plot shows the number of associated terms for a non-overlapping ", + "sliding window of 500 genes along the ranking of ubiquity using ", + "our default parameters. The terms have been obtained using a ", + "gene set enrichment analysis with the tool ", + "g:Profiler. We observe that the most ", + "ubiquitous genes have many more known biological implications ", + "than any other bucket of genes. The genes of average ubiquity ", + "have almost no associations with GeneOntology terms. The number ", + "of associations rises again for the least ubiquitous genes." + ))), + p(HTML(paste0( + "Note: Click on the legend items to toggle single sources. A ", + "double-click will isolate a single source of interest." + ))), + plotly::plotlyOutput("gsea_plot_ranking", height = "600px") + ) ) ) ) diff --git a/scripts/gsea.R b/scripts/gsea.R index e0d0edb..6fb92ca 100644 --- a/scripts/gsea.R +++ b/scripts/gsea.R @@ -45,3 +45,6 @@ fig <- plotly::plot_ly() |> ) plotly::save_image(fig, image_path, width = 1200, height = 800) + +gsea_plot_ranking <- fig +usethis::use_data(gsea_plot_ranking, internal = TRUE, overwrite = TRUE)