tooltip and other ui changes, #62

rnabioco · Feb 27, 2021 · 62db42a · 62db42a
1 parent 542f199
commit 62db42a
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Showing 3 changed files with 66 additions and 32 deletions.
diff --git a/global.R b/global.R
@@ -11,6 +11,7 @@ library(rsconnect)
 library(ExperimentHub)
 library(Seurat)
 library(shinydashboard)
+library(bsplus)
 library(dashboardthemes)
 library(tidyverse)
 library(data.table)

diff --git a/server.R b/server.R
@@ -100,6 +100,15 @@ server <- function(input, output, session) {
       h4("")
     )
   )
+
+  w9 <- Waiter$new(
+    id = "someta",
+    html = tagList(
+      spin_flower(),
+      h4("Preview loading..."),
+      h4("")
+    )
+  )
 
   data1 <- reactive({
 
@@ -318,9 +327,10 @@ server <- function(input, output, session) {
   })
 
   output$ref_summary <- renderUI({
-    HTML(paste0("cell types: ", ncol(data3()),
+    HTML(paste0("<b>", "cell types: ", ncol(data3()),
                 "<br>",
-                "genes: ", nrow(data3())))
+                "genes: ", nrow(data3()),
+                "<b>"))
   })
 
   data3b <- reactive({
@@ -813,7 +823,7 @@ server <- function(input, output, session) {
     if (length(input$someta_cell_clicked) != 0) {
       sel <- input$someta_cell_clicked
       rv$lastgeo <- someta$id[sel$row]
-      w6$show()
+      w9$show()
       rv$links <- list_geo(rv$lastgeo)
       message(rv$links)
       if (rv$links != "error_get") {
@@ -836,7 +846,7 @@ server <- function(input, output, session) {
       }
 
       url <- str_c("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=", input$geoid)
-      w6$hide()
+      w9$hide()
       showModal(modalDialog(
         size = "l",
         div(id = "modalfiles",

diff --git a/ui.R b/ui.R
@@ -29,6 +29,7 @@ ui <- dashboardPage(
         tabName = "dashboard",
         # js stuff ----
         useShinyjs(),
+        use_bs_tooltip(),
         tags$head(
           tags$script(HTML(js2))
         ),
@@ -65,9 +66,10 @@ ui <- dashboardPage(
 
         # load example data ----
         actionButton("example",
-                     "load example data",
+                     "Load example data",
                      icon = icon("space-shuttle")
-        ),
+        ) %>%
+          bs_embed_tooltip("Use example data from GSE113049 for walkthrough", placement = "right"),
 
         # Horizontal line ----
         tags$hr(),
@@ -118,7 +120,7 @@ ui <- dashboardPage(
       ),
       tabItem(
         tabName = "matrixLoad",
-        h2("Load UMI Counts Matrix"),
+        h2("Load Counts (raw or normalized) Matrix"),
         # Input: Select a file ----
         fileInput("file1", "Choose Matrix File",
                   multiple = TRUE,
@@ -130,22 +132,27 @@ ui <- dashboardPage(
                     ".tsv",
                     ".rds",
                     ".rda",
-                    ".rdata"
+                    ".rdata",
+                    ".gz"
                   )
-        ),
+        ) %>% 
+          bs_embed_tooltip("Accepted file types: plain or gz text files, and rds/rda/rdata for Seurat/SCE",
+                           placement = "right"),
 
         # GEO id load ----
         actionButton("geo1",
                      "or from GEO id",
-                     icon = icon("search")),
+                     icon = icon("search")) %>% 
+          bs_embed_tooltip("Alternatively, load data directly from GEO with ID", placement = "right"),
 
         actionButton("matrixPopup", "Display UMI Matrix in popup"),
+        tags$hr(),
         DTOutput("contents1"), # UMI Count Matrix
         tags$hr()
       ),
       tabItem(
         tabName = "metadataLoad",
-        h2("Load Metadata table"),
+        h2("Load Metadata"),
         fileInput("file2", "Choose Metadata File",
                   multiple = FALSE,
                   accept = c(
@@ -156,21 +163,27 @@ ui <- dashboardPage(
                     ".tsv",
                     ".rds",
                     ".rda",
-                    ".rdata"
+                    ".rdata",
+                    ".gz"
                   )
-        ),
+        ) %>% 
+          bs_embed_tooltip("Accepted file types: plain or gz text files, and rds/rda/rdata for Seurat/SCE",
+                           placement = "right"),
 
         # GEO id load ----
         actionButton("geo2",
                      "or from GEO id",
-                     icon = icon("search")),
+                     icon = icon("search")) %>% 
+          bs_embed_tooltip("Alternatively, load data directly from GEO with ID", placement = "right"),
 
         actionButton("metadataPopup", "Display Metadata table in popup"),
-        h2("Choose column in metadata with cluster information"),
-        selectInput("metadataCellType", "Cell Type Metadata Column:",
+        h2("Choose column in metadata with cluster info"),
+        selectInput("metadataCellType", NULL,
                     choice = list("")
-        ),
-        fluidRow(column(12, DTOutput('contents2'))),
+        ) %>% 
+          bs_embed_tooltip("Select from dropdown, or click on preview column below", placement = "right"),
+        tags$hr(),
+        DTOutput('contents2'),
         #DT::dataTableOutput("contents2"), # Metadata table
         tags$hr(),
         uiOutput("colclicked")
@@ -185,10 +198,12 @@ ui <- dashboardPage(
                       "ref_cortex_dev", "ref_pan_indrop", "ref_pan_smartseq2",
                       "ref_mouse_atlas"
                     )
-        ),
+        ) %>% 
+          bs_embed_tooltip("Select from pre-built references in clustifyrdatahub", placement = "right"),
         actionButton("ref_linkgo",
                      label = "Go to original source",
-                     icon = icon("link")),
+                     icon = icon("link")) %>% 
+          bs_embed_tooltip("For more info on the reference datasets", placement = "right"),
         tags$hr(),
         h2("Or load reference table"),
         fileInput("file3", "Choose Reference Average Expression File",
@@ -197,14 +212,16 @@ ui <- dashboardPage(
                     "text/csv",
                     "text/comma-separated-values,text/plain",
                     ".csv",
-                    ".xlsx",
                     ".tsv",
-                    ".rds",
-                    ".rda"
+                    ".xlsx",
+                    ".gz"
                   )
-        ),
+        ) %>% 
+          bs_embed_tooltip("Alternatively, choose local file of average gene expression by cell type", placement = "right"),
+        tags$hr(),
+        uiOutput("ref_summary"),
         DTOutput("contents3", height = "300px"),
-        uiOutput("ref_summary")
+        tags$hr()
       ),
       tabItem(
         tabName = "clustifyres",
@@ -214,20 +231,26 @@ ui <- dashboardPage(
             solidHeader = TRUE,
             status = "info",
             title = "clustifyr messages",
-            htmlOutput("clustifym")),
-        downloadButton("downloadReference", "Download average expression matrix"),
-        downloadButton("downloadClustify", "Download clustify results matrices"),
+            htmlOutput("clustifym")) %>% 
+          bs_embed_tooltip("Console messages from run", "right"),
+        div(style="display:inline-block",
+          downloadButton("downloadReference", "Download average expression matrix") %>% 
+            bs_embed_tooltip("Note: this is the same file needed to use the current dataset as reference in the future", "bottom"),
+          downloadButton("downloadClustify", "Download clustify results matrices") %>% 
+            bs_embed_tooltip("Cell type inference as sheet1, correlation matrix as sheet2, of xlsx", "bottom")
+        ),
         # actionButton("uploadClustify", "Upload reference matrix"),
-        h2("average matrix"),
+        h2("Average Expression Matrix"),
         DT::dataTableOutput("reference", height = "300px"), # Reference Matrix
         tags$hr(),
-        h2("ranked correlation matrix"), 
+        h2("Ranked Correlation Matrix"), 
         DT::dataTableOutput("clustify", height = "300px"), # Clustify Matrix
         tags$hr(),
-        h2("cell type results"),
+        h2("Cell Type Inference Results"),
         DT::dataTableOutput("corToCall", height = "300px"),
         tags$hr(),
-        plotOutput("hmap", height = "900px")
+        plotOutput("hmap", height = "900px"),
+        tags$hr(),
       ),
       tabItem(
         tabName = "someta",