Initial commit

.Rbuildignore

@@ -0,0 +1,19 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^data-raw$
+^revdep$
+^notes$
+^pkgdown$
+^README\.Rmd$
+^LICENSE\.md$
+^SECURITY\.md$
+^_pkgdown\.yml$
+^\.covrignore$
+^\.github$
+^Makefile$
+^cran-comments\.md$
+^CRAN-SUBMISSION$
+^vignettes/articles$
+^\.lintr$
+^\.github$
+^Meta$

.Rinstignore

@@ -0,0 +1,2 @@
+WORDLIST
+create-plotr-objects\.R

.github/.gitignore

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

.github/ISSUE_TEMPLATE/feature_template.md

@@ -0,0 +1,37 @@
+---
+name: Feature request
+about: Make a case for a new feature in SomaPlotr
+labels: feature
+---
+
+## Checks
+- [ ] Please search previous issues before creating a new
+  one, to ensure yours is not a duplicate
+- [ ] The proposed feature fits in the scope of SomaPlotr
+  data visualization of SomaScan.
+
+
+## Problem
+Please briefly describe the problem you have encountered ...
+
+
+## Feature
+Please briefly describe the proposed new feature and
+how it solves the problem above ...
+
+
+## R code
+Please add more evidence with R code if appropriate ...
+
+```r
+# insert reprex here
+```
+
+## Priority Level
+- [ ] High
+- [ ] Medium
+- [ ] Low
+
+---
+
+Thanks for contributing :partying_face:!

.github/ISSUE_TEMPLATE/issue_template.md

@@ -0,0 +1,52 @@
+---
+name: Bug report
+about: Describe the bug you've encountered
+labels: bug
+---
+
+## Checks
+- [ ] Please search previous issues before creating a new one,
+  to ensure yours is not a duplicate. You can
+  [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/),
+  `is:pr`, `is:closed`, etc., as needed, e.g. you'd simply remove `is:open` to
+  search _all_ issues in the repo, open or closed.
+- [ ] Please include a minimal reproducible example (AKA a `reprex`)
+
+If you've never heard of a [reprex](http://reprex.tidyverse.org/) before,
+please start by reading <https://www.tidyverse.org/help/#reprex>.
+
+---
+
+
+## Description
+Please briefly describe the problem you have encountered
+and what output you expected ...
+
+
+## Output
+```r
+# insert reprex of what you see here 
+```
+
+## Expected Output
+```r
+# insert reprex of what you *expected* to see here 
+```
+
+## Steps
+Please describe any steps you have already taken that may
+assist in reproducing the (unexpected) behavior:
+
+- bullet 1
+- bullet 2
+- bullet 3
+
+
+## Priority Level
+- [ ] High
+- [ ] Medium
+- [ ] Low
+
+---
+
+Thanks for reporting :partying_face:!

.github/ISSUE_TEMPLATE/question_template.md

@@ -0,0 +1,38 @@
+---
+name: Question
+about: Ask a question about SomaPlotr
+labels: question
+---
+
+- You are using `SomaPlotr` :partying_face: ... but have hit a road block :weary:
+- Please search previous issues before creating a new one,
+  to ensure yours is not a duplicate. You can
+  [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/),
+  `is:pr`, `is:closed`, etc., as needed, e.g. you'd simply remove `is:open` to
+  search _all_ issues in the repo, open or closed.
+
+---
+
+
+## Description
+Brief description of the problem ... use bullets if necessary:
+
+- bullet 1
+- bullet 2
+- bullet 3
+
+
+Please describe your question with R code if appropriate:
+
+```r
+# insert code here
+```
+
+## Priority Level
+- [ ] High
+- [ ] Medium
+- [ ] Low
+
+---
+
+Thank you for using `SomaPlotr` :pray:!

.github/SUPPORT.md

@@ -0,0 +1,49 @@
+# Getting help with SomaPlotr
+
+Thanks for using SomaPlotr!
+
+Before filing an issue, there are a few places to explore
+and pieces to put together to make the process as smooth as possible.
+
+## Make a reprex
+
+If we can’t reproduce the bug, we can’t fix it!
+Start by making a minimal **repr**oducible **ex**ample using the  [reprex](https://reprex.tidyverse.org/) package. 
+If you haven't heard of or used `reprex` before, you're in for a treat! 
+Seriously, `reprex` will make all of your R-question-asking endeavors easier
+(which is an excellent ROI for the five to ten minutes it'll take you to learn what it's all about). 
+For additional `reprex` pointers, check out the [Get help!](https://www.tidyverse.org/help/).
+
+## Where to ask?
+
+Armed with your `reprex`, the next step is to figure out [where to ask](https://www.tidyverse.org/help/#where-to-ask). 
+
+* If it's a `R` related question: start with [community.rstudio.com](https://community.rstudio.com/)
+  and/or [StackOverflow](https://stackoverflow.com). There are more people there to answer questions.  
+
+* If it's a bug with [SomaPlotr](https://github.com/SomaLogic/SomaPlotr/): you're
+  in the right place; please [file an issue](https://github.com/SomaLogic/SomaPlotr/issues/new).
+
+* If you're not sure: let the community help you figure it out! 
+  If your problem _is_ a bug or a feature request, you can easily return
+  [here](https://github.com/SomaLogic/SomaPlotr/issues/) and report it. 
+
+* For _non_-coding related feedback or inquiries please reach out to <techsupport@somalogic.com>.
+
+Before opening a new issue, be sure to
+[search issues and pull requests](https://github.com/SomaLogic/SomaPlotr/issues/)
+to make sure the bug hasn't been reported and/or already fixed in the development version. 
+By default, the search will be pre-populated with `is:issue is:open`. 
+You can [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/),
+`is:pr`, `is:closed`, etc., as needed, e.g. you'd simply remove `is:open` to
+search _all_ issues in the repo, open or closed.
+
+## What happens next?
+
+We aim to respond to questions or simple bugs within 24 - 48h, particularly
+questions accompanied by a `reprex` can typically be addressed quickly.
+More complex bugs or feature requests can take longer, as they require a
+deeper discussion regarding the software development lifecycle of `SomaPlotr`.
+As mentioned above, you may always reach out to our Global Scientific Engagement
+team at <techsupport@somalogic.com> or for more general inquiries at <support@somalogic.com>.
+

.github/pull_request_template.md

@@ -0,0 +1,51 @@
+
+## Overview of Pull Request
+
+General description of the purpose for this pull request ...
+
+Fixes #<issue_number>
+
+### Main changes
+
+- bullet 1
+- bullet 2
+
+### Change type
+
+Please check the relevant box(es):
+
+- [ ] New feature (no API change; @amanda-hi, @stufield)
+- [ ] Bug fix (no API change -> fixes an issue; @amanda-hi, @stufield)
+- [ ] Breaking change (fix or feature with API change; @amanda-hi, @stufield)
+- [ ] Documentation update (@SLbmangum, @kmurugesan14)
+- [ ] Package maintenance (structural, non-code, non-breaking changes; @stufield)
+- [ ] README change (@SLbmangum, @kmurugesan14, @nmcnabbSL)
+- [ ] LICENSE changes (@SLbmangum)
+
+### Choose reviewer(s)
+
+- [ ] @amanda-hi
+- [ ] @stufield
+- [ ] @SLbmangum
+- [ ] @kmurugesan14
+- [ ] @nmcnabbSL
+
+### Reviewer by Department
+
+| Department     | Reviewer      | Change Type          |
+|:-------------- |:------------- | -------------------- |
+| Bioinformatics | @amanda-hi    | Code, bugs, features |
+|                | @stufield     | bugs, features       |
+| Legal          | @SLbmangum    | LICENSE              | 
+| Product        | @kmurugesan14 | Documentation        |
+| Regulatory     | @nmcnabbSL    | Documentation        |
+
+------------
+
+### Code
+
+If appropriate, please add any relevant code ...
+
+```r
+head(mtcars)
+```

.github/workflows/check-standard.yaml

@@ -0,0 +1,81 @@
+# 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
+    paths:
+      - 'DESCRIPTION'
+      - 'NAMESPACE'
+      - 'R/**'
+      - 'tests/testthat/test-**.R'
+  pull_request:
+    branches:
+      - main
+      - master
+    paths:
+      - '.Rbuildignore'
+      - '.Rinstignore'
+      - 'DESCRIPTION'
+      - 'NAMESPACE'
+      - 'R/**'
+      - 'tests/testthat/test-**.R'
+      - 'vignettes/**'
+  workflow_dispatch:
+
+name: R-CMD-check
+
+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: 'release'}
+          #- {os: ubuntu-latest, r: 'oldrel-1'}
+          # comment out the 'devel' testing for odd-numbered BioConductor versions, e.g. v3.15
+          #   this typically is the case between April-October
+          #- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      R_KEEP_PKG_SOURCE: yes
+      TZ: 'America/Denver'
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          dependencies: '"all"'
+          cache: false
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::knitr
+            any::remotes
+            any::rmarkdown
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran", "--no-build-vignettes", "--timings")'
+          build_args: 'c("--no-manual", "--no-resave-data")'
+          upload-snapshots: false
+          upload-results: false
+          error-on: '"warning"'
+          check-dir: '"check"'

.github/workflows/document.yaml

@@ -0,0 +1,43 @@
+on: workflow_dispatch
+
+name: Document
+
+jobs:
+  document:
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          clean: true
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::roxygen2
+          needs: roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE DESCRIPTION
+          git commit -m "Update documentation" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin