Initial commit

R/app.R

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+#' Run the application server.
+#'
+#' @param port The port to serve the application on.
+#'
+#' @export
+run_app <- function(port = 3464) {
+    runApp(shinyApp(ui, server), port = port)
+}

R/data.R

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+#' A `data.table` containig data on genes and their expression behavior.
+"genes"

R/server.R

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+#' Server implementing the main user interface.
+#' @noRd
+server <- function(input, output) {
+    output$all_data <- DT::renderDataTable({
+        data <- ubigen::genes[, .(
+            "Gene" = glue::glue_data(
+                ubigen::genes,
+                "<a href=\"https://www.ensembl.org/Homo_sapiens/Gene/Summary",
+                "?db=core;g={gene}\" target=\"_blank\">{hgnc_name}</a>"
+            ),
+            "Rank" = rank,
+            "Score" = score,
+            "Median" = median_expression,
+            "Mean" = mean_expression,
+            "Standard deviation" = sd_expression,
+            "Expressed" = above_zero,
+            "Above 50 TPM" = above_threshold,
+            "Above median" = above_median,
+            "Above 95%" = above_95
+        )]
+
+        DT::datatable(
+            data,
+            options = list(pageLength = 100),
+            rownames = FALSE,
+            escape = FALSE
+        ) |>
+            DT::formatPercentage(c(
+                "Score",
+                "Expressed",
+                "Above 50 TPM",
+                "Above median",
+                "Above 95%"
+            )) |>
+            DT::formatRound(c(
+                "Median",
+                "Mean",
+                "Standard deviation"
+            ))
+    })
+}

R/ui.R

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+#' Function for creating the main user interface.
+#' @noRd
+ui <- function() {
+    navbarPage(
+        theme = bslib::bs_theme(
+            version = 5,
+            bootswatch = "united",
+            primary = "#7d19bf"
+        ),
+        title = "Ubigen",
+        tabPanel(
+            "Explore",
+            sidebarLayout(
+                sidebarPanel(
+                    width = 3,
+                ),
+                mainPanel(
+                    width = 9,
+                )
+            )
+        ),
+        tabPanel(
+            title = "Data",
+            DT::dataTableOutput("all_data")
+        ),
+        tabPanel(
+            title = "Publication"
+        )
+    )
+}

R/utils.R

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+#' Various things that should be imported into the package namespace.
+#'
+#' @importFrom data.table :=
+#' @importFrom data.table .BY
+#' @importFrom data.table .EACHI
+#' @importFrom data.table .GRP
+#' @importFrom data.table .I
+#' @importFrom data.table .N
+#' @importFrom data.table .NGRP
+#' @importFrom data.table .SD
+#' @importFrom data.table data.table
+#'
+#' @import shiny
+NULL