Initial commit

.BBSoptions

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+UnsupportedPlatforms: win32

.Rbuildignore

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+^vitessceAnalysisR\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
+^\.BBSoptions$
+^.github$
+^package\.json$
+^package-lock\.json$
+^node_modules$
+^img$
+^webpack\.config\.js$
+^inst/htmlwidgets/lib/.*$
+^inst/htmlwidgets/dist/.*\.map$
+^inst/testdata
+^index\.md$
+^LICENSE\.md$
+^pkgdown$
+^vignettes$
+^docs$
+^pkgdown$
+^data$
+^check$

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: An existing feature does not work
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Environment:**
+ - Release or git hash: 
+ - Operating system: 
+ - R version: 
+ - RStudio version: 

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: feature
+assignees: ''
+
+---
+
+**User story**
+
+**Preferred solution**
+
+**Possible alternatives**

.github/workflows/deploy.yml

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+name: R
+
+on: [push, pull_request]
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    env:
+      cache-version: 8
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up libraries for Ubuntu
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libsodium-dev libharfbuzz-dev libfribidi-dev libcurl4-openssl-dev texlive-latex-base texlive-fonts-extra pandoc libmagick++-dev libhdf5-dev
+
+      - name: Set up R 4.0
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 4.0
+      - name: Get R and OS version
+        id: get-version
+        run: |
+          cat("::set-output name=os-version::", sessionInfo()$running, "\n", sep = "")
+          cat("::set-output name=r-version::", R.Version()$version.string, "\n", sep = "")
+          cat("::endgroup::\n")
+        shell: Rscript {0}
+      - name: Cache dependencies
+        id: cache-deps
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}/*
+          key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ env.cache-version }}-deps
+      - name: Install dependencies
+        if: steps.cache-deps.outputs.cache-hit != 'true'
+        run: |
+          install.packages(c("remotes", "rcmdcheck", "BiocManager", "Seurat", "covr"))
+          BiocManager::install("BiocCheck")
+          remotes::install_github(c("RubD/Giotto", "mojaveazure/seurat-disk"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      - name: rcmdcheck
+        run: |
+          rcmdcheck::rcmdcheck(
+            error_on = "warning",
+            check_dir = "check"
+          )
+        shell: Rscript {0}
+        env:
+          _R_CHECK_FORCE_SUGGESTS_: false
+      - name: BiocCheck
+        run: |
+          BiocCheck::BiocCheck(
+            dir('check', 'tar.gz$', full.names = TRUE),
+            `no-check-R-ver` = TRUE,
+            `no-check-pkg-size` = TRUE,
+            `no-check-vignettes` = TRUE
+          )
+        shell: Rscript {0}
+        env:
+          _R_CHECK_FORCE_SUGGESTS_: false
+      - name: Run covr
+        run: |
+          covr::package_coverage()
+        shell: Rscript {0}
+      - name: Downgrade pkgdown
+        run: |
+          remotes::install_version("pkgdown", "2.0.3")
+        shell: Rscript {0}
+      - name: Build docs
+        run: |
+          Rscript -e 'pkgdown::build_site(new_process = FALSE)'
+          touch docs/.nojekyll
+      - uses: actions/upload-pages-artifact@v1
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          path: ./docs
+  deploy:
+    runs-on: ubuntu-22.04
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        id: deployment
+        uses: actions/deploy-pages@v1

.gitignore

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+.Rproj.user
+.DS_Store
+.Rhistory
+*.Rcheck/
+*.tar.gz
+node_modules/
+docs/
+tests/testthat/seurat/
+data/
+check/
+vignettes/data/
+*.Rproj
+.RData

DESCRIPTION

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+Package: vitessceAnalysisR
+Type: Package
+Title: Data preparation helper functions for usage with the vitessceR library.
+Version: 0.99.0
+Authors@R: c(
+    person(
+      given = "Mark",
+      family = "Keller",
+      email = "mark_keller@g.harvard.edu",
+      role = c("cre", "aut"),
+      comment = c(ORCID = "0000-0003-3003-874X")
+    )
+  )
+Description:
+  The R API contains
+  classes and functions for loading single-cell data stored as
+  SingleCellExperiment, SpatialExperiment, and Seurat objects.
+biocViews: SingleCell, Spatial
+License: MIT + file LICENSE
+BugReports: https://github.com/vitessce/vitessceAnalysisR/issues
+URL: https://github.com/vitessce/vitessceAnalysisR
+Encoding: UTF-8
+LazyData: false
+Language: en-US
+StagedInstall: no
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+VignetteBuilder: knitr
+Imports:
+    Matrix,
+    DelayedArray,
+    htmlwidgets,
+    jsonlite,
+    R6,
+    plumber,
+    future,
+    httpuv,
+    stringr,
+    reticulate,
+    varhandle,
+    tools,
+    stats,
+    methods,
+    S4Vectors,
+    grDevices,
+    basilisk,
+    zellkonverter,
+    SummarizedExperiment,
+    SingleCellExperiment,
+    SpatialExperiment
+Suggests: 
+    testthat,
+    knitr,
+    covr,
+    bslib,
+    pkgdown,
+    rmarkdown,
+    purrr,
+    rjson,
+    Seurat,
+    SeuratDisk,
+    Giotto

LICENSE

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+YEAR: 2020
+COPYRIGHT HOLDER: Gehlenborg Lab

LICENSE.md

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+# MIT License
+
+Copyright (c) 2020 Gehlenborg Lab
+
+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(AbstractWrapper)
+export(Component)
+export(CoordinationType)
+export(DataType)
+export(FileType)
+export(GiottoWrapper)
+export(MultiImageWrapper)
+export(OmeTiffWrapper)
+export(SCEWrapper)
+export(SPEWrapper)
+export(SeuratWrapper)
+export(VitessceConfig)
+export(get_giotto_obj)
+export(get_sce_obj)
+export(get_seurat_obj)
+export(get_spe_obj)
+export(giotto_to_anndata_zarr)
+export(hconcat)
+export(obj_list)
+export(render_vitessce)
+export(sce_to_anndata_zarr)
+export(seurat_to_anndata_zarr)
+export(spe_to_anndata_zarr)
+export(spe_to_ome_zarr)
+export(vconcat)
+export(vitessce_output)
+export(vitessce_widget)
+import(R6)
+import(plumber)
+importFrom(SingleCellExperiment,"reducedDims<-")
+importFrom(SingleCellExperiment,int_colData)
+importFrom(SingleCellExperiment,reducedDims)
+importFrom(SpatialExperiment,"colData<-")
+importFrom(SpatialExperiment,getImg)
+importFrom(SummarizedExperiment,colData)
+importFrom(grDevices,as.raster)
+importFrom(grDevices,col2rgb)
+importFrom(methods,new)
+importFrom(methods,slot)
+importFrom(stats,rnorm)
+importFrom(stats,rpois)
+importFrom(stats,runif)

NEWS.md

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+# vitessceR 0.99.0 (2023-09-19)
+
+* Initial Bioconductor submission
+
+# vitessceR 0.0.0 (early development version)
+

R/basilisk.R

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+#' The Python environment
+#'
+#' Defines a conda environment via Basilisk, which is used
+#' to convert R objects to Zarr stores.
+#' This environment has been adapted from zellkonverter::.AnnDataDependencies.
+#' Reference: https://bioconductor.org/packages/release/bioc/vignettes/basilisk/inst/doc/motivation.html
+#'
+#' @keywords internal
+py_env <- basilisk::BasiliskEnvironment(
+  envname="vitessce_basilisk_env",
+  pkgname="vitessceR",
+  packages=c(
+    "numpy==1.*",
+    "pandas==1.*",
+    "anndata==0.7.*",
+    "h5py==3.*",
+    "hdf5==1.*",
+    "natsort==7.*",
+    "packaging==20.*",
+    "scipy==1.*",
+    "sqlite==3.*",
+    "zarr==2.*",
+    "numcodecs==0.*"
+  ),
+  pip=c(
+    "ome-zarr==0.2.1"
+  )
+)