feat(iatlas): import github.com/CRI-iAtlas/iatlas-app (ARCH-362)

apps/iatlas/app/.Rbuildignore

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+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+.gitlab-ci.yml
+^\.Rprofile$
+
+Dockerfile.build
+css
+global.R
+index.html
+init.R
+install_and_init.R
+markdown
+rsconnect
+server.R
+ui.R
+www
+^\.github$

apps/iatlas/app/.Rprofile

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+if (file.exists("renv/activate.R")) {
+  source("renv/activate.R")
+
+  cat("
+--------------------------------------------------------------------------------
+Welcome to the CRI iAtlas Shiny App
+--------------------------------------------------------------------------------
+\n")
+
+  if (length(find.package("devtools", quiet=T)) == 0 || length(find.package("renv", quiet=T)) == 0) {
+    # prompt instead since RStudio won't show progress for slow .RProfile scripts...
+    cat("TODO: Install package requirements. This may take up to an hour the first time.\n")
+    cat("RUN: source('./install_and_init.R')\n")
+  } else {
+    # auto-run since it should be quick, but makes sure any new requirements are installed.
+    source('./install_and_init.R')
+  }
+} else if (Sys.getenv("R_CONFIG_ACTIVE") == "shinyapps") {
+  cat("
+--------------------------------------------------------------------------------
+CRI iAtlas Shiny App: Production
+--------------------------------------------------------------------------------
+\n")
+  source('./init.R')
+}
+
+# For Ubuntu 18.04 (also known as Bionic)
+options(repos = c(
+  REPO_NAME = "https://packagemanager.rstudio.com/all/__linux__/bionic/latest",
+  getOption("repos")
+))
+
+# For Ubuntu 20.04 (also known as Focal)
+options(repos = c(
+  REPO_NAME = "https://packagemanager.rstudio.com/all/__linux__/focal/latest",
+  getOption("repos")
+))
+
+if (interactive()) {
+  suppressMessages(require(devtools))
+  suppressMessages(require(testthat))
+  suppressMessages(require(usethis))
+}

apps/iatlas/app/.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store
+rsconnect/
+tests/testthat/helper-a_use_dev_globals.R
+.mailmap
+inst/extdata/*
+tracks
+app_config.yml

apps/iatlas/app/DESCRIPTION

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+Package: iatlas.app
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R:
+    person(given = "First",
+           family = "Last",
+           role = c("aut", "cre"),
+           email = "first.last@example.com",
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Suggests:
+    crayon,
+    devtools,
+    memoise (>= 2.0),
+    renv,
+    rsconnect,
+    testthat (>= 3.0.0),
+    usethis
+Config/testthat/edition: 3
+RoxygenNote: 7.2.0
+biocViews:
+Imports:
+    arrow,
+    broom,
+    caret,
+    concordanceIndex,
+    cyjShiny,
+    dplyr,
+    DT,
+    ggplot2,
+    ggmosaic,
+    glmnet,
+    grDevices,
+    grid,
+    grImport2,
+    iatlasGraphQLClient,
+    iatlas.modules,
+    iatlas.modules2,
+    igvShiny,
+    ImmuneSubtypeClassifier,
+    lazyeval,
+    magrittr,
+    plotly,
+    pROC,
+    purrr,
+    RColorBrewer,
+    readr,
+    rlang,
+    sortable,
+    shiny,
+    shinycssloaders,
+    shinydashboard,
+    shinyjs,
+    stringr,
+    survival,
+    survminer,
+    tibble,
+    tidyr,
+    tidyselect,
+    utils,
+    viridis,
+    wrapr
+Remotes:
+    CRI-iAtlas/iatlasGraphQLClient@main,
+    CRI-iAtlas/iatlas.modules@master,
+    CRI-iAtlas/iatlas.modules2@master,
+    CRI-iAtlas/ImmuneSubtypeClassifier@master,
+    th86/concordanceIndex@master,
+    cytoscape/cyjShiny@master,
+    paul-shannon/igvShiny@master

apps/iatlas/app/Dockerfile

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+FROM r-base:4.2.3
+
+# Install supporting packages
+RUN apt-get -y update && apt-get -y --no-install-recommends install \
+    build-essential \
+    gettext-base \
+    libcurl4-openssl-dev \
+    libnode-dev \
+    libpq-dev \
+    libssl-dev \
+    libv8-dev \
+    libxml2-dev \
+    postgresql-client-16 \
+  # Cleanup
+  && apt-get -y autoclean \
+  && apt-get -y autoremove \
+  && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /opt/app
+COPY renv.lock .
+COPY renv/activate.R renv/activate.R
+
+# Resolve dependencies
+RUN R -e "options(pkgType = 'binary'); install.packages('V8', type = 'source')"
+# RUN R -e "options(pkgType='binary'); source('renv/activate.R'); renv::restore()"

apps/iatlas/app/LICENSE

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+YEAR: 2022
+COPYRIGHT HOLDER: CRI iAtlas Developers

apps/iatlas/app/LICENSE.md

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+# MIT License
+
+Copyright (c) 2022 CRI iAtlas Developers
+
+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.

apps/iatlas/app/NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+importFrom(dplyr,filter)
+importFrom(dplyr,pull)
+importFrom(dplyr,select)
+importFrom(dplyr,slice)
+importFrom(magrittr,"%>%")
+importFrom(rlang,.data)

apps/iatlas/app/R/barplot.R

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+create_barplot <- function(
+  df,
+  x_col = "x",
+  y_col = "y",
+  error_col = "error",
+  key_col = NA,
+  color_col = NA,
+  label_col = NA,
+  xlab = "",
+  ylab = "",
+  title = "",
+  source_name = NULL,
+  bar_colors = NULL,
+  showlegend = T) {
+
+  if(is.na(key_col)) key_col <- x_col
+  if(is.na(color_col)) color_col <- x_col
+  if(is.na(label_col)) label_col <- x_col
+
+  if (is.null(bar_colors)) {
+    bar_colors <- viridis::viridis_pal(option = "D")(dplyr::n_distinct(df[[color_col]]))
+  }
+  wrapr::let(
+    alias = c(
+      X = x_col,
+      Y = y_col,
+      KEY = key_col,
+      COLOR = color_col,
+      ERROR = error_col,
+      LABEL = label_col),
+    plotly::plot_ly(
+      df,
+      x = ~X,
+      y = ~Y,
+      color = ~COLOR,
+      text = ~LABEL,
+      textposition = 'none',
+      key = ~KEY,
+      type = 'bar',
+      source = source_name,
+      colors = bar_colors,
+      error_y = list(
+        array = ~ERROR,
+        color = 'black',
+        thickness = 1),
+      hoverinfo = 'text',
+      showlegend = showlegend
+    )) %>%
+    plotly::layout(
+      legend = list(orientation = 'h', x = 0, y = 1),
+      title = title,
+      xaxis = list(title = xlab),
+      yaxis = list(title = ylab)
+    ) %>%
+    format_plotly()
+
+}
+
+create_barplot_horizontal <- function(df,
+                            x_col = "x",
+                            y_col = "y",
+                            error_col = "error",
+                            key_col = NA,
+                            color_col = NA,
+                            label_col = NA,
+                            order_by = NULL,
+                            xlab = "",
+                            ylab = "",
+                            title = "",
+                            showLegend = TRUE,
+                            legendTitle = " ",
+                            source_name = NULL,
+                            bar_colors = NULL){
+  if(is.na(key_col)) key_col <- x_col
+  if(is.na(color_col)) color_col <- x_col
+  if(is.na(label_col)) label_col <- x_col
+
+  if (is.null(bar_colors)) {
+    bar_colors <- viridis::viridis_pal(option = "D")(dplyr::n_distinct(df[[color_col]]))
+  }
+  wrapr::let(
+    alias = c(
+      X = x_col,
+      Y = y_col,
+      KEY = key_col,
+      COLOR = color_col,
+      ERROR = error_col,
+      LABEL = label_col),
+    plotly::plot_ly(
+      df,
+      x = ~X,
+      y = ~Y,
+      color = ~COLOR,
+      text = ~LABEL,
+      textposition = 'none',
+      key = ~KEY,
+      type = 'bar',
+      source = source_name,
+      colors = bar_colors,
+      orientation = 'h',
+      error_x = list(
+        visible = T,
+        type = "data",
+        array = ~ERROR,
+        color = 'black',
+        thickness = 1),
+      hoverinfo = 'text'
+    )) %>%
+    plotly::layout(
+      title = title,
+      xaxis = list(title = xlab),
+      yaxis = list(title = ylab,
+                   categoryorder = "array",
+                   categoryarray = ~order_by),
+      showlegend = showLegend,
+      legend = list(orientation = 'h', x = 0, y = 1,
+                    title = list(text = legendTitle)
+        )
+    ) %>%
+    format_plotly()
+
+}