Merge pull request #2 from jumpingrivers/main

WP4: re-factor app

.Rbuildignore

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+^tfpbrowser\.Rproj$
+^\.Rproj\.user$
+.lintr
+^data-raw$
+^\.github$
+^LICENSE\.md$
+_\.new\.png$

.github/.gitignore

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+*.html

.github/workflows/R-CMD-check.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/lint.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+# {shinytest2}: Ignore new debug snapshots for `$expect_values()`
+*_.new.png

.lintr

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+linters: linters_with_defaults(
+    assignment_linter = NULL,
+    object_name_linter = NULL,
+    line_length_linter = line_length_linter(120),
+    undesirable_operator_linter = undesirable_operator_linter(
+      modify_defaults(
+        default_undesirable_operators,
+        "<-" = "Use =, not <-, for assignment."
+      )
+    )
+  )
+exclusions: list("renv/")

DESCRIPTION

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+Package: tfpbrowser
+Title: Builds Shiny application for 'tfpscanner' outputs
+Version: 0.0.6
+Authors@R: 
+    person("Jumping", "Rivers", , "[email protected]", role = c("aut", "cre"))
+Description: An R package to contain the code for the Shiny app to explore the 
+  outputs from the 'tfpscanner' package.
+License: MIT + file LICENSE
+Depends: 
+    R (>= 4.0.0)
+Imports:
+    bslib,
+    dplyr,
+    fs,
+    ggplot2,
+    ggiraph,
+    glue,
+    htmltools,
+    janitor,
+    magrittr,
+    reactable,
+    readr,
+    rlang,
+    shiny,
+    shinyjs,
+    stringr,
+    tibble,
+    tidyr
+Suggests:
+    shinytest2,
+    testthat,
+    usethis
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.2
+LazyData: true

LICENSE

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+YEAR: 2022
+COPYRIGHT HOLDER: tfpbrowser authors

LICENSE.md

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+# MIT License
+
+Copyright (c) 2022 tfpbrowser authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export("%>%")
+export(run_app)
+importFrom(magrittr,"%>%")
+importFrom(rlang,.data)
+importFrom(rlang,.env)

NEWS.md

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+# tfpbrowser 0.0.6 _2022-11-08_
+
+- Switch to using rds inputs instead of html inputs
+- Use {ggiraph} widget as input to folder selection
+- Add functions to parse tooltip and extract cluster id
+- Remove unnecessary html files
+
+# tfpbrowser 0.0.5 _2022-11-02_
+
+- Move panels from RHS to collapsible above
+- Rearrange content of collapsible panel
+- Add CSS file to style collapsible
+- Remove mutation drop down for now
+
+# tfpbrowser 0.0.4 _2022-10-19_
+
+- Add module to download RDS files
+
+# tfpbrowser 0.0.3 _2022-09-24_
+
+- Split into modules
+
+# tfpbrowser 0.0.2 _2022-09-06_
+
+- add {shinytest2} tests
+
+# tfpbrowser 0.0.1 _2022-09-05_
+
+- initialise R package
+- convert ui and server scripts to functions
+- add data into package
+- minor fixes to pass R CMD check
+

R/add_ext_resources.R

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+#' Add external resources to the shiny app
+#'
+#' Function is internally used to add external
+#' resources inside the Shiny application.
+add_ext_resources = function() {
+  shiny::addResourcePath(
+    "www", system.file("app/www", package = "tfpbrowser", mustWork = TRUE)
+  )
+  shiny::tags$head(
+    shinyjs::useShinyjs(),
+    shiny::tags$link(rel = "stylesheet", type = "text/css", href = "www/tfpbrowser-style.css")
+  )
+}

R/app_server.R

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+#' Shiny application server
+#' @param input,output,session Internal parameters for `{shiny}`.
+#' @noRd
+app_server = function(input, output, session) {
+
+  # Load mutation selectize options on server-side
+  # (quicker loading on slower browsers)
+  # This is because there is a lot of options
+  # client-side processing is slow
+  shiny::updateSelectizeInput(session,
+                       "mutations",
+                       choices = get_unique_mutations(
+                         system.file("app", "www", "data",
+                                     "sarscov2-audacity-westerncape2021.csv",
+                                     package = "tfpbrowser",
+                                     mustWork = TRUE)),
+                       server = TRUE)
+
+
+
+  # Load treeview -----------------------------------------------------------
+
+  # create plotly output from saved ggplot2 outputs
+  output$treeview = ggiraph::renderGirafe({
+    filename = get_filename(input$widgetChoice)
+    g = readRDS(filename)
+    tooltip_css = paste0(
+      "background-color:black;",
+      "color:grey;",
+      "padding:14px;",
+      "border-radius:8px;",
+      "font-family:\"Courier New\",monospace;"
+    )
+    suppressWarnings(ggiraph::girafe(ggobj = g,
+                    options = list(
+                      ggiraph::opts_selection(
+                        type = "single"),
+                      ggiraph::opts_sizing(
+                        width = 0.8),
+                      ggiraph::opts_tooltip(
+                        css = tooltip_css,
+                        use_fill = FALSE)
+                      )
+                    ))
+  })
+
+  # get selected cluster id based on widget choice
+  selected_cluster_id = shiny::reactive({
+    get_selected_cluster_id(widgetChoice = input$widgetChoice,
+                            treeviewSelected = input$treeview_selected)
+  })
+
+  # output result of click
+  output$select_text = shiny::renderText({
+    paste("You have selected cluster ID:", selected_cluster_id())
+  })
+
+  # Tables Tab --------------------------------------------------------------
+  tablesServer(
+    "table1",
+    cluster_choice = selected_cluster_id
+  )
+
+  # Plots Tab ----------------------------------------------------------
+  plotsServer(
+    "plot1",
+    cluster_choice = selected_cluster_id
+  )
+
+  # RDS Tab ----------------------------------------------------------
+  rdsServer(
+    "rds1",
+    cluster_choice = selected_cluster_id
+  )
+
+} # end server function

R/app_ui.R

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+#' Shiny application user interface
+#'
+#' @param request Internal parameter for `{shiny}`.
+#' @noRd
+app_ui = function(request) {
+  shiny::tagList(
+
+    shinyjs::useShinyjs(),
+
+    shiny::navbarPage(
+      # title
+      title = "tfpbrowser",
+
+      header = add_ext_resources(),
+      # theme
+      theme = bslib::bs_theme(version = 4,
+                              bootswatch = "minty",
+                              bg = "#EBEEEE",
+                              fg = "#002147",
+                              primary = "#003E74",
+                              secondary = "#9D9D9D"),
+
+      # Input widgets
+      shiny::tabPanel(
+        title = "Data",
+
+        shiny::fluidRow(
+          shiny::column(12,
+                        # use details and summary to create expandable section
+                        htmltools::tags$details(
+                          # preview of expandable section
+                          htmltools::tags$summary("Download Files (click to expand)"),
+
+                          shiny::br(),
+
+                          # text to print choice
+                          shiny::textOutput("select_text"),
+                          shiny::br(),
+
+                          # output options
+                          shiny::tabsetPanel(id = "plot_tabs",
+
+                                             # Tables tab
+                                             tablesUI("table1"),
+
+                                             # Plots tab
+                                             plotsUI("plot1"),
+
+                                             # RDS tab
+                                             rdsUI("rds1")
+
+                          )
+                        )
+                        )
+          ), # end fluid row
+
+        # Bottom row - show tree (static html output from tfpscanner)
+        shiny::fluidRow(
+
+          shiny::column(12,
+
+            # choose type of treeviw
+            shiny::radioButtons(inputId = "widgetChoice",
+                                label = "Select treeview",
+                                choices = c(
+                                  "Logistic growth rate",
+                                  "Simple logistic growth rate",
+                                  "Simple trait log odds"),
+                                inline = TRUE),
+
+            # show treeview widget
+            shiny::wellPanel(
+              ggiraph::girafeOutput("treeview"),
+              style = "background: white",
+            ),
+            shiny::br()
+          )
+        ) # end fluid row
+      ), # end "data" page
+
+      # about page
+      shiny::tabPanel(
+        title = "About",
+        shiny::includeMarkdown(system.file("app", "www", "content", "about.md",
+                                           package = "tfpbrowser",
+                                           mustWork = TRUE))
+        )
+
+    ) # end navbar page
+  ) # end tag list
+
+}