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7 changed files with 25 additions and 178 deletions
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@ -1,6 +1,6 @@
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Package: geposanui
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Title: Graphical user interface for geposan
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Version: 1.1.0
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Version: 1.0.1
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Authors@R:
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person(
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"Elias",
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2
R/app.R
2
R/app.R
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@ -91,7 +91,7 @@ ui <- function(options) {
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HTML(glue::glue(
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"<code>geposanui</code> version {packageVersion(\"geposanui\")}<br>",
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"GitHub: <a href=\"https://github.com/johrpan/geposanui/\" ",
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"target=\"blank\">johrpan/geposanui</a><br>",
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"target=\"blank\">johrpan/geposan</a><br>",
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"Citation: <a href=\"https://doi.org/10.1093/nargab/lqae037\" ",
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"target=\"blank\">10.1093/nargab/lqae037</a>"
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))
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@ -32,18 +32,6 @@ comparison_editor_ui <- function(id, options) {
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NS(id, "comparison_genes")
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),
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gene_selector_ui(NS(id, "custom_genes"))
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),
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tabsetPanel(
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id = NS(id, "warning_panel"),
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type = "hidden",
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tabPanelBody(value = "hide"),
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tabPanelBody(
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value = "show",
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div(
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style = "color: orange; margin-bottom: 16px;",
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htmlOutput(NS(id, "warnings"))
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)
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)
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)
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)
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}
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@ -61,72 +49,18 @@ comparison_editor_server <- function(id, preset, options) {
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moduleServer(id, function(input, output, session) {
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custom_gene_ids <- gene_selector_server("custom_genes")
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comparison_warnings <- reactiveVal(character())
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output$warnings <- renderUI({
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HTML(paste(comparison_warnings(), collapse = "<br>"))
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})
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observe({
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updateTabsetPanel(
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session,
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"warning_panel",
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selected = if (is.null(comparison_warnings())) "hide" else "show"
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)
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})
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reactive({
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new_warnings <- character()
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if (input$comparison_genes == "Random genes") {
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preset <- preset()
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gene_pool <- preset$gene_ids
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reference_gene_ids <- preset$reference_gene_ids
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gene_pool <- gene_pool[!gene_pool %chin% reference_gene_ids]
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gene_ids <- if (input$comparison_genes == "Random genes") {
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gene_pool[sample(length(gene_pool), length(reference_gene_ids))]
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} else if (input$comparison_genes == "Your genes") {
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custom_gene_ids()
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} else {
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options$comparison_gene_sets[[input$comparison_genes]]
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}
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excluded_reference_gene_ids <-
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gene_ids[gene_ids %chin% reference_gene_ids]
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if (length(excluded_reference_gene_ids) > 0) {
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excluded_reference_genes <-
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geposan::genes[id %chin% excluded_reference_gene_ids]
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excluded_reference_genes[is.na(name), name := id]
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new_warnings <- c(new_warnings, paste0(
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"The following genes have been excluded because they are already ",
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"part of the reference genes: ",
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paste(
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excluded_reference_genes$name,
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collapse = ", "
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)
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))
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}
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excluded_gene_ids <- gene_ids[!gene_ids %chin% gene_pool]
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if (length(excluded_gene_ids) > 0) {
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excluded_genes <-
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geposan::genes[id %chin% excluded_gene_ids]
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excluded_genes[is.na(name), name := id]
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new_warnings <- c(new_warnings, paste0(
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"The following genes are not present in the results: ",
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paste(
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excluded_genes$name,
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collapse = ", "
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)
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))
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}
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comparison_warnings(new_warnings)
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gene_ids[!gene_ids %chin% reference_gene_ids & gene_ids %chin% gene_pool]
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})
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})
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}
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13
R/details.R
13
R/details.R
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@ -86,6 +86,19 @@ details_server <- function(id, options, results) {
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"Percentile"
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)
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output_data <- reactive({
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filtered_results()[, ..columns][
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,
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distance := paste0(
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format(
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round(distance / 1000000, digits = 2),
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nsmall = 2,
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),
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" Mbp"
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)
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]
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})
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output$download <- downloadHandler(
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filename = "geposan_filtered_results.csv",
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content = \(file) fwrite(filtered_results()[, ..columns], file = file),
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@ -102,8 +102,8 @@ preset_editor_ui <- function(id, options) {
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"reference genes to find patterns in their ",
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"chromosomal positions. If you would like to apply ",
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"this method for your own research, see ",
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"<a href=\"https://github.com/johrpan/geposanui/blob/main/README.md\" ",
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"target=\"_blank\">this page</a> for ",
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"<a href=\"https://code.johrpan.de/johrpan/geposanui/src/",
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"branch/main/README.md\" target=\"_blank\">this page</a> for ",
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"more information."
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))
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}
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@ -196,6 +196,7 @@ preset_editor_server <- function(id, options) {
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),
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warning = function(w) {
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new_warnings <<- c(new_warnings, w$message)
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}
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)
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95
R/results.R
95
R/results.R
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@ -32,31 +32,7 @@ results_ui <- function(id, options) {
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plotly::plotlyOutput(
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NS(id, "rank_plot"),
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width = "100%",
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height = "500px"
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)
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),
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tabsetPanel(
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id = NS(id, "comparison_results_panel"),
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type = "hidden",
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tabPanelBody(value = "hide"),
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tabPanelBody(
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value = "show",
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div(
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style = paste0(
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"display: flex; gap: 16px; align-items: center; ",
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"margin-top: 16px"
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),
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div("Detailed results for the selected comparison genes"),
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downloadButton(
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NS(id, "download_comparison_results"),
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"Download CSV",
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class = "btn-outline-primary"
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)
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),
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div(
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style = "margin-top: 16px; margin-bottom: 8px;",
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DT::DTOutput(NS(id, "comparison_results"))
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)
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height = "600px"
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)
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)
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),
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@ -269,73 +245,6 @@ results_server <- function(id, options, analysis) {
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geposan::plot_scores(ranking(), gene_sets = gene_sets)
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})
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observe({
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updateTabsetPanel(
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session,
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"comparison_results_panel",
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selected = if (length(comparison_gene_ids()) > 0) "show" else "hide"
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)
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})
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methods <- options$methods
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method_ids <- sapply(methods, function(method) method$id)
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method_names <- sapply(methods, function(method) method$name)
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columns <- c(
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"rank",
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"gene",
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"name",
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"chromosome",
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"distance",
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method_ids,
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"score",
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"percentile"
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)
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column_names <- c(
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"",
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"Gene",
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"",
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"Chr.",
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"Distance",
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method_names,
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"Score",
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"Percentile"
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)
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results_filtered_comparison <- reactive({
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results()[gene %chin% comparison_gene_ids()]
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})
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output$download_comparison_results <- downloadHandler(
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filename = "geposan_results_custom.csv",
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content = \(file) fwrite(
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results_filtered_comparison()[, ..columns],
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file = file
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),
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contentType = "text/csv"
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)
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output$comparison_results <- DT::renderDT({
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data <- results_filtered_comparison()[, ..columns]
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data[, distance := glue::glue(
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"{format(round(distance / 1000000, digits = 2), nsmall = 2)} Mbp"
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)]
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DT::datatable(
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data,
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rownames = FALSE,
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colnames = column_names,
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options = list(
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rowCallback = js_link(),
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columnDefs = list(list(visible = FALSE, targets = 2)),
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pageLength = 25
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)
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) |>
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DT::formatRound(c(method_ids, "score"), digits = 4) |>
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DT::formatPercentage("percentile", digits = 2)
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})
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output$rankings_plot <- plotly::renderPlotly({
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preset <- preset()
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@ -451,7 +360,7 @@ results_server <- function(id, options, analysis) {
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preset()$reference_gene_ids
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)
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comparison <- if (length(comparison_gene_ids()) > 0) {
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comparison <- if (!is.null(comparison_gene_ids())) {
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geposan::compare(ranking(), comparison_gene_ids())
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}
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@ -28,16 +28,6 @@ h5 {
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font-weight: normal;
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}
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.navbar[data-bs-theme="light"] {
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--bslib-navbar-light-bg: #1964BF;
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--bs-navbar-color: rgba(255, 255, 255, 0.65);
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--bs-navbar-hover-color: rgba(255, 255, 255, 0.8);
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--bs-navbar-disabled-color: rgba(255, 255, 255, 0.3);
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--bs-navbar-active-color: #fff;
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--bs-navbar-brand-color: #fff;
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--bs-navbar-brand-hover-color: #fff;
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}
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/* Fix slider inputs floating above dropdown menu */
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.irs--shiny .irs-bar {
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z-index: 1;
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