Merge pull request #19 from getwilds/dev

Packaging the App (Closes #6)

.Rbuildignore

@@ -1,2 +1,7 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^data-raw$
+^LICENSE\.md$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,51 @@
+# 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:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          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
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.gitignore

@@ -3,3 +3,9 @@
 .RData
 .Ruserdata
 .DS_Store
+renv/library/
+renv/staging/
+renv/cache/
+inst/doc
+.Rprofile
+.Renviron

DESCRIPTION

@@ -1,11 +1,52 @@
 Package: oncarto
 Type: Package
-Title: What the Package Does (Title Case)
+Title: Oncology Cartographer
 Version: 0.1.0
-Author: Who wrote it
-Maintainer: The package maintainer <[email protected]>
-Description: More about what it does (maybe more than one line)
-    Use four spaces when indenting paragraphs within the Description.
-License: What license is it under?
+Authors@R: 
+    c(person(given = "Vivek",
+           family = "Sriram",
+           email = "[email protected]",
+           role = c("aut"),
+           comment = c(ORCID = "0000-0003-3759-2911")),
+    person(given = "Sean",
+           family = "Kross",
+           email = "[email protected]",
+           role = c("ctb", "cre"),
+           comment = c(ORCID = "0000-0001-5215-0316")),
+    person(given = "Monica",
+           family = "Gerber",
+           email = "[email protected]",
+           role = c("ctb"),
+           comment = c(ORCID = "0000-0001-9878-9166")),
+    person(given = "Scott",
+           family = "Chamberlain",
+           email = "[email protected]",
+           role = c("ctb"),
+           comment = c(ORCID = "0000-0003-1444-9135"))
+    )
+Description: Oncarto (Oncology Cartographer) is an R package / Shiny dashboard
+    developed by the Fred Hutch Data Science Lab (DaSL) for the
+    automated integration and visualization of publicly available cancer
+    incidence data for the Fred Hutch Cancer Center catchment area.
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
+RoxygenNote: 7.3.2
+Roxygen: list(markdown = TRUE)
+Suggests: 
+    knitr,
+    rmarkdown,
+    testthat (>= 3.0.0)
+VignetteBuilder: knitr
+Imports:
+    dplyr,
+    htmltools,
+    leaflet,
+    sf,
+    shiny,
+    shinycssloaders,
+    shinydashboard,
+    tigris
+Depends: 
+    R (>= 2.10)
+Config/testthat/edition: 3

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: oncarto authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 oncarto 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

@@ -1 +1,41 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(example_callback)
+export(oncarto_file)
+export(run_app)
+importFrom(dplyr,filter)
+importFrom(dplyr,left_join)
+importFrom(htmltools,HTML)
+importFrom(htmltools,a)
+importFrom(htmltools,tags)
+importFrom(leaflet,addLegend)
+importFrom(leaflet,addPolygons)
+importFrom(leaflet,addTiles)
+importFrom(leaflet,colorNumeric)
+importFrom(leaflet,highlightOptions)
+importFrom(leaflet,labelOptions)
+importFrom(leaflet,leaflet)
+importFrom(leaflet,leafletOutput)
+importFrom(sf,st_transform)
+importFrom(shiny,NS)
+importFrom(shiny,addResourcePath)
+importFrom(shiny,column)
+importFrom(shiny,fluidRow)
+importFrom(shiny,includeMarkdown)
+importFrom(shiny,moduleServer)
+importFrom(shiny,renderUI)
+importFrom(shiny,selectInput)
+importFrom(shiny,shinyApp)
+importFrom(shiny,uiOutput)
+importFrom(shinycssloaders,withSpinner)
+importFrom(shinydashboard,box)
+importFrom(shinydashboard,dashboardBody)
+importFrom(shinydashboard,dashboardHeader)
+importFrom(shinydashboard,dashboardPage)
+importFrom(shinydashboard,dashboardSidebar)
+importFrom(shinydashboard,menuItem)
+importFrom(shinydashboard,sidebarMenu)
+importFrom(shinydashboard,tabItem)
+importFrom(shinydashboard,tabItems)
+importFrom(tigris,counties)
+importFrom(utils,read.table)

R/example-callback.R

@@ -0,0 +1,22 @@
+#' A function that provides an example dataframe for testing.
+#' @param key A string used internally (in a specific shiny server module
+#' implementation) to indicate which data to return.
+#' @export
+#' @importFrom utils read.table
+#' @examples
+#' example_callback("county-incidence")
+#'
+example_callback <- function(key) {
+  stopifnot(key %in% c("county-incidence", "contact-info"))
+
+  if (key == "county-incidence") {
+    utils::read.table(
+      header = TRUE,
+      system.file(file.path("test", "example-incidence.tsv"), package = "oncarto"),
+      sep = "\t"
+    )
+  } else if (key == "contact-info") {
+    oncarto_file("fh-contact-info.md")
+  }
+}
+

R/get-county-boundaries.R

@@ -0,0 +1,14 @@
+# Get the right county boundaries for the desired choropleth visualization
+#' @importFrom tigris counties
+#' @importFrom sf st_transform
+#'
+get_county_boundaries <- function(state_abbr, county_col_name) {
+  # Get county boundaries for the choropleth visualization using the tigris package
+  out <- sf::st_transform(
+    tigris::counties(state = state_abbr, class = "sf"),
+    crs = 4326
+  )
+
+  out[[county_col_name]] <- out[['NAMELSAD']]
+  out
+}

R/global.R

@@ -0,0 +1 @@
+utils::globalVariables(c("NAMELSAD", "cancer_type", "race", "sex", "age", "stage", "year"))

R/make-leaflet.R

@@ -0,0 +1,41 @@
+# Make the choropleth map
+#' @importFrom leaflet leaflet addTiles addPolygons addLegend labelOptions
+#' highlightOptions
+#'
+make_leaflet <- function(in_data, in_palette, incidence_col_name,
+                         county_col_name, legend_title) {
+
+  leaflet::leaflet(data = in_data) |>
+    leaflet::addTiles() |>
+    leaflet::addPolygons(
+      fillColor = ~in_palette(
+        in_data[[incidence_col_name]]
+      ),
+      weight = 1,
+      opacity = 1,
+      color = "white",
+      dashArray = "3",
+      fillOpacity = 0.7,
+      highlightOptions = leaflet::highlightOptions(
+        weight = 3,
+        color = "#666",
+        dashArray = "",
+        fillOpacity = 0.7,
+        bringToFront = TRUE
+      ),
+      label = ~paste(in_data[[county_col_name]], ": ",
+                     in_data[[incidence_col_name]]),
+      labelOptions = leaflet::labelOptions(
+        style = list("font-weight" = "normal", padding = "3px 8px"),
+        textsize = "15px",
+        direction = "auto"
+      )
+    ) |>
+    leaflet::addLegend(
+      pal = in_palette,
+      values = ~in_data[[incidence_col_name]],
+      opacity = 0.7,
+      title = legend_title,
+      position = "topright"
+    )
+}

R/make-palette.R

@@ -0,0 +1,12 @@
+# Generate palette for choropleth map
+#' @importFrom leaflet colorNumeric
+#'
+make_palette <- function(in_data, col_name, lower_color, upper_color,
+                         na_color) {
+
+  leaflet::colorNumeric(
+    c(lower_color, upper_color),
+    domain = in_data[[col_name]],
+    na.color = na_color
+  )
+}

R/oncarto-body.R

@@ -0,0 +1,6 @@
+# This function fills in the body of the shiny dashboard
+#' @importFrom shinydashboard dashboardBody
+#'
+oncarto_body <- function() {
+
+}

R/oncarto-file.R

@@ -0,0 +1,23 @@
+#' Get the paths to files installed with oncarto
+#'
+#' This function allows you to quickly access files that are installed with
+#' oncarto.
+#'
+#' @param path The name of the file. If no argument is provided then
+#' all of the example files will be listed.
+#'
+#' @return A vector of file paths
+#' @export
+#' @examples
+#' oncarto_file()
+#'
+oncarto_file <- function(path = NULL){
+  if(is.null(path)) {
+    list.files(
+      system.file(c("app"), package = "oncarto"),
+      full.names = TRUE)
+  } else {
+    system.file(c("app"), path, package = "oncarto",
+                mustWork = TRUE)
+  }
+}

R/oncarto-header.R

@@ -0,0 +1,14 @@
+# This function fills in the header of the shiny dashboard
+#' @importFrom shinydashboard dashboardHeader
+#' @importFrom htmltools tags
+#'
+oncarto_header <- function(title, logo_src, logo_href, logo_width, logo_height) {
+  shinydashboard::dashboardHeader(
+    title = htmltools::tags$a(
+      href = logo_href,
+      tags$img(
+        src = logo_src, height = logo_height, width = logo_width
+      )
+    )
+  )
+}

R/oncarto-sidebar.R

@@ -0,0 +1,19 @@
+# This function fills in the sidebar of the shiny dashboard
+#' @importFrom shinydashboard dashboardSidebar sidebarMenu menuItem
+#'
+oncarto_sidebar <- function() {
+  shinydashboard::dashboardSidebar(
+    shinydashboard::sidebarMenu(
+      # Multiple tabs, each correspond to a different type of map / info
+      shinydashboard::menuItem(
+        "Cancer Incidence by County",
+        tabName = "county-incidence"
+      ),
+
+      shinydashboard::menuItem(
+        "Background",
+        tabName = "background"
+      )
+    )
+  )
+}