mirror of
https://github.com/johrpan/ubigen.git
synced 2025-10-26 19:57:24 +01:00
Reformat to use two spaces for tabs
This commit is contained in:
parent
6aefa55eb9
commit
80d81c572d
3 changed files with 219 additions and 219 deletions
2
R/app.R
2
R/app.R
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@ -5,5 +5,5 @@
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#'
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#' @export
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run_app <- function(host = "127.0.0.1", port = 3464) {
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runApp(shinyApp(ui, server), host = host, port = port)
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runApp(shinyApp(ui, server), host = host, port = port)
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}
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220
R/server.R
220
R/server.R
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@ -1,43 +1,43 @@
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#' Server implementing the main user interface.
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#' @noRd
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server <- function(input, output) {
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ranked_data <- reactive({
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total_weight <- abs(input$above_zero) +
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abs(input$above_median) +
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abs(input$above_95) +
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abs(input$mean_expression) +
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abs(input$sd_expression)
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ranked_data <- reactive({
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total_weight <- abs(input$above_zero) +
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abs(input$above_median) +
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abs(input$above_95) +
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abs(input$mean_expression) +
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abs(input$sd_expression)
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data <- data.table::copy(ubigen::genes)
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data <- data.table::copy(ubigen::genes)
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data[, score :=
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(input$above_zero * above_zero +
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input$above_95 * above_95 +
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input$above_median * above_median +
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input$mean_expression * mean_expression_normalized +
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input$sd_expression * sd_expression_normalized) /
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total_weight]
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data[, score :=
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(input$above_zero * above_zero +
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input$above_95 * above_95 +
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input$above_median * above_median +
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input$mean_expression * mean_expression_normalized +
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input$sd_expression * sd_expression_normalized) /
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total_weight]
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data.table::setorder(data, -score)
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data[, rank := .I]
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data[, percentile := 1 - rank / max(rank)]
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data.table::setorder(data, -score)
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data[, rank := .I]
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data[, percentile := 1 - rank / max(rank)]
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data
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})
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data
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})
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output$scores_plot <- plotly::renderPlotly(scores_plot(ranked_data()))
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output$scores_plot <- plotly::renderPlotly(scores_plot(ranked_data()))
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output$selected_genes <- DT::renderDataTable({
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selected_points <- plotly::event_data("plotly_selected")
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output$selected_genes <- DT::renderDataTable({
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selected_points <- plotly::event_data("plotly_selected")
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data <- if (is.null(selected_points)) {
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ranked_data()
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} else {
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ranked_data()[rank %in% selected_points$x]
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}
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data <- if (is.null(selected_points)) {
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ranked_data()
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} else {
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ranked_data()[rank %in% selected_points$x]
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}
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genes_table(data)
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})
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genes_table(data)
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})
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}
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#' Create plot showing the distribution of scores using `plotly`.
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@ -49,95 +49,95 @@ server <- function(input, output) {
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#' @return A `plotly` figure for rendering.
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#' @noRd
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scores_plot <- function(ranked_data, ranks = 1000) {
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data <- if (is.null(ranks)) {
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ranked_data
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} else {
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ranked_data[1:ranks]
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}
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data <- if (is.null(ranks)) {
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ranked_data
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} else {
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ranked_data[1:ranks]
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}
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ranks_label <- if (is.null(ranks)) {
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"Ranks"
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} else {
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glue::glue("Ranks (1 to {ranks})")
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}
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ranks_label <- if (is.null(ranks)) {
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"Ranks"
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} else {
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glue::glue("Ranks (1 to {ranks})")
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}
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plotly::plot_ly() |>
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plotly::add_markers(
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data = data,
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x = ~rank,
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y = ~score,
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text = ~hgnc_name,
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customdata = ~percentile,
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hovertemplate = paste0(
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"<b>%{text}</b><br>",
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"Rank: %{x}<br>",
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"Score: %{y:.2}<br>",
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"Percentile: %{customdata:.2%}",
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"<extra></extra>"
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)
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) |>
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plotly::layout(
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xaxis = list(title = ranks_label),
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yaxis = list(title = "Score"),
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clickmode = "event+select",
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dragmode = "select"
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)
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plotly::plot_ly() |>
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plotly::add_markers(
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data = data,
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x = ~rank,
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y = ~score,
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text = ~hgnc_name,
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customdata = ~percentile,
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hovertemplate = paste0(
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"<b>%{text}</b><br>",
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"Rank: %{x}<br>",
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"Score: %{y:.2}<br>",
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"Percentile: %{customdata:.2%}",
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"<extra></extra>"
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)
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) |>
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plotly::layout(
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xaxis = list(title = ranks_label),
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yaxis = list(title = "Score"),
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clickmode = "event+select",
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dragmode = "select"
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)
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}
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#' Create a displayable data table from the gene results data.
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#' @noRd
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genes_table <- function(data) {
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data <- data[, .(
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"Gene" = glue::glue_data(
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data,
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"<a href=\"https://www.ensembl.org/Homo_sapiens/Gene/Summary",
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"?db=core;g={gene}\" target=\"_blank\">{hgnc_name}</a>"
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),
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"Rank" = rank,
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"Percentile" = percentile,
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"Score" = score,
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"Median" = median_expression,
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"Mean" = mean_expression,
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"Standard deviation" = sd_expression,
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"Expressed" = above_zero,
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"Above median" = above_median,
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"Above 95%" = above_95
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)]
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data <- data[, .(
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"Gene" = glue::glue_data(
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data,
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"<a href=\"https://www.ensembl.org/Homo_sapiens/Gene/Summary",
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"?db=core;g={gene}\" target=\"_blank\">{hgnc_name}</a>"
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),
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"Rank" = rank,
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"Percentile" = percentile,
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"Score" = score,
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"Median" = median_expression,
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"Mean" = mean_expression,
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"Standard deviation" = sd_expression,
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"Expressed" = above_zero,
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"Above median" = above_median,
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"Above 95%" = above_95
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)]
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DT::datatable(
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data,
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options = list(
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buttons = list(
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list(
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extend = "copy",
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text = "Copy to clipboard"
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),
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list(
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extend = "csv",
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text = "Download CSV"
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)
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),
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dom = "fBrtip",
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pageLength = 100
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DT::datatable(
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data,
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options = list(
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buttons = list(
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list(
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extend = "copy",
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text = "Copy to clipboard"
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),
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rownames = FALSE,
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escape = FALSE,
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selection = "none",
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extensions = "Buttons"
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list(
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extend = "csv",
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text = "Download CSV"
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)
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),
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dom = "fBrtip",
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pageLength = 100
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),
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rownames = FALSE,
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escape = FALSE,
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selection = "none",
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extensions = "Buttons"
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) |>
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DT::formatPercentage(
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c(
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"Percentile",
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"Score",
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"Expressed",
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"Above median",
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"Above 95%"
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),
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digits = 2,
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) |>
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DT::formatPercentage(
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c(
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"Percentile",
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"Score",
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"Expressed",
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"Above median",
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"Above 95%"
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),
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digits = 2,
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) |>
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DT::formatRound(c(
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"Median",
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"Mean",
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"Standard deviation"
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))
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DT::formatRound(c(
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"Median",
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"Mean",
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"Standard deviation"
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))
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}
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216
R/ui.R
216
R/ui.R
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@ -1,115 +1,115 @@
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#' Function for creating the main user interface.
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#' @noRd
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ui <- function() {
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navbarPage(
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theme = bslib::bs_theme(
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version = 5,
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bootswatch = "united",
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primary = "#7d19bf"
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navbarPage(
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theme = bslib::bs_theme(
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version = 5,
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bootswatch = "united",
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primary = "#7d19bf"
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),
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title = "Ubigen",
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tabPanel(
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"Explore",
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sidebarLayout(
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sidebarPanel(
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width = 3,
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h3("Features"),
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sliderInput(
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"above_zero",
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verticalLayout(
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strong("Expressed"),
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paste0(
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"Percentage of samples in which the gene is ",
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"expressed."
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)
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = 0.33
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),
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sliderInput(
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"above_median",
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verticalLayout(
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strong("Expressed above median"),
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paste0(
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"Percentage of samples that express the gene ",
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"more than the median of expression within ",
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"that sample."
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)
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = 0.33
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),
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sliderInput(
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"above_95",
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verticalLayout(
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strong("Expressed above 95%"),
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paste0(
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"Percentage of samples that express the gene ",
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"more than the 95. percentile of expression ",
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"within that sample."
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)
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = 0.33
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),
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sliderInput(
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"mean_expression",
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verticalLayout(
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strong("Mean expression"),
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div(paste0(
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"Average of the gene's expression across all ",
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"samples."
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))
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = 1.0
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),
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sliderInput(
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"sd_expression",
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verticalLayout(
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strong("Standard deviation"),
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paste0(
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"Standard deviation of the gene's expression ",
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"across all samples."
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)
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = -1.0
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)
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),
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title = "Ubigen",
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tabPanel(
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"Explore",
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sidebarLayout(
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sidebarPanel(
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width = 3,
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h3("Features"),
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sliderInput(
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"above_zero",
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verticalLayout(
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strong("Expressed"),
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paste0(
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"Percentage of samples in which the gene is ",
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"expressed."
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)
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = 0.33
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),
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sliderInput(
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"above_median",
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verticalLayout(
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strong("Expressed above median"),
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paste0(
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"Percentage of samples that express the gene ",
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"more than the median of expression within ",
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"that sample."
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)
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = 0.33
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),
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sliderInput(
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"above_95",
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verticalLayout(
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strong("Expressed above 95%"),
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paste0(
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"Percentage of samples that express the gene ",
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"more than the 95. percentile of expression ",
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"within that sample."
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)
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = 0.33
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),
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sliderInput(
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"mean_expression",
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verticalLayout(
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strong("Mean expression"),
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div(paste0(
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"Average of the gene's expression across all ",
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"samples."
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))
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = 1.0
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),
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sliderInput(
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"sd_expression",
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verticalLayout(
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strong("Standard deviation"),
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paste0(
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"Standard deviation of the gene's expression ",
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"across all samples."
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)
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),
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min = -1.0,
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max = 1.0,
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step = 0.01,
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value = -1.0
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)
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),
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mainPanel(
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width = 9,
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h3("Distribution of scores"),
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div(paste0(
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"Click or drag within the figure to select genes of ",
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"interest."
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)),
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plotly::plotlyOutput("scores_plot"),
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h3("Detailed ranking"),
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div(paste0(
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"Click on gene names to view them using the Ensembl ",
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"genome browser."
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)),
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div(class = "p-1"),
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DT::dataTableOutput("selected_genes")
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)
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)
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),
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tabPanel(
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title = "Help"
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),
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tabPanel(
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title = "Publication"
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mainPanel(
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width = 9,
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h3("Distribution of scores"),
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div(paste0(
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"Click or drag within the figure to select genes of ",
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"interest."
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)),
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plotly::plotlyOutput("scores_plot"),
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h3("Detailed ranking"),
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div(paste0(
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"Click on gene names to view them using the Ensembl ",
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"genome browser."
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)),
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div(class = "p-1"),
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DT::dataTableOutput("selected_genes")
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)
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)
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),
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tabPanel(
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title = "Help"
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),
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tabPanel(
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title = "Publication"
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)
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)
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}
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