Merge pull request #75 from ncborcherding/dev

V1.99.0 Overhaul

.Rbuildignore

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+^\.github$
+^www$

.Rhistory

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+library(Ibex)
+data("ibex_example")
+ibex_example <- runIbex(ibex_example,
+chains = "heavy",
+method = "encoder",
+encoder.model = "VAE",
+encoder.input = "AF",
+reduction.name = "Heavy_VAE_AF")
+ibex_example <- runIbex(ibex_example,
+chains = "Heavy",
+method = "encoder",
+encoder.model = "VAE",
+encoder.input = "AF",
+reduction.name = "Heavy_VAE_AF")
+library(Ibex)
+data("ibex_example")
+set.seed(42)
+ibex_example <- runIbex(ibex_example,
+chains = "Heavy",
+method = "encoder",
+encoder.model = "VAE",
+encoder.input = "AF",
+reduction.name = "Heavy_VAE_AF")
+ibex_example <- runIbex(trex_example,
+chains = "Light",
+method = "encoder",
+encoder.model = "AE",
+encoder.input = "KF",
+reduction.name = "Light_AE_KF")
+ibex_example <- runIbex(ibex_example,
+chains = "Light",
+method = "encoder",
+encoder.model = "AE",
+encoder.input = "KF",
+reduction.name = "Light_AE_KF")
+ibex_example <- runIbex(ibex_example,
+chains = "Heavy",
+method = "encoder",
+encoder.model = "VAE",
+encoder.input = "OHE",
+reduction.name = "Heavy_VAE_OHE")
+saveRDS(ibex_example@reductions$Heavy_VAE_AF@cell.embeddings, "~/runIbex_Heavy_VAE_AF_reduction.rds")
+saveRDS(ibex_example@reductions$Light_AE_KF@cell.embeddings, "~/runIbex_Light_AE_KF_reduction.rds")
+saveRDS(ibex_example@reductions$Heavy_VAE_OHE@cell.embeddings, "~/runIbex_Heavy_VAE_OHE_reduction.rds")
+setwd("~/Documents/GitHub/Ibex")
+spelling::spell_check_package()
+dim(ibex_example)
+spelling::spell_check_package()
+devtools::document()
+spelling::spell_check_package()
+devtools::document()
+spelling::spell_check_package()
+spelling::update_wordlist()
+testthat::test_local()
+testthat::test_local()
+devtools::check()
+setwd("~/Documents/GitHub/escape")
+devtools::check()
+suppressPackageStartupMessages(library(escape))
+suppressPackageStartupMessages(library(SingleCellExperiment))
+suppressPackageStartupMessages(library(Seurat))
+suppressPackageStartupMessages(library(SeuratObject))
+pbmc_small <- get("pbmc_small")
+pbmc_small <- DietSeurat(suppressMessages(UpdateSeuratObject(pbmc_small)))
+sce <- as.SingleCellExperiment(pbmc_small, assay = "RNA")
+GS.hallmark <- getGeneSets(library = "H")
+data("escape.gene.sets", package="escape")
+gene.sets <- escape.gene.sets
+gene.sets <- list(Tcell_signature = c("CD2","CD3E","CD3D"),
+Myeloid_signature = c("SPI1","FCER1G","CSF1R"))
+devtools::check()
+ES.seurat <- enrichIt(obj = pbmc_small,
+gene.sets = GS.hallmark,
+groups = 1000,
+cores = 2,
+min.size = 5)
+ES.sce <- enrichIt(obj = sce,
+gene.sets = GS.hallmark,
+method = "UCell",
+groups = 1000,
+cores = 2,
+min.size = 5)
+usethis::use_bioc_badge()
+use_github_action_check_standard(
+save_as = "R-CMD-check.yaml",
+ref = NULL,
+ignore = TRUE,
+open = FALSE
+)
+library(usethis)
+use_github_action_check_standard(
+save_as = "R-CMD-check.yaml",
+ref = NULL,
+ignore = TRUE,
+open = FALSE
+)

.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: ${{ 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@v3
+
+      - 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

.github/workflows/pr-commands.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:
+  issue_comment:
+    types: [created]
+
+name: Commands
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test-coverage.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: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

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 Package: escape
 Title: Easy single cell analysis platform for enrichment
-Version: 1.9.0
-Date: 2022-3-05
+Version: 1.99.0
+Date: 2024-02-18
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"),
     person(given = "Jared", family = "Andrews", role = c("aut"), email = "jared.andrews07@gmail.com"))
-Description: A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize GSEA across individual cells. 
-License: GPL-2
+Description: A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize ssGSEA, GSVA, AUCell, and UCell-based enrichment calculations across individual cells. 
+License: MIT + file LICENSE 
 Encoding: UTF-8
 LazyData: false
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.1
 biocViews: Software, SingleCell, Classification, Annotation, GeneSetEnrichment, Sequencing, GeneSignaling, Pathways
 Depends: R (>= 4.1)
 Imports: 
-	grDevices,  
-	dplyr, 
-	ggplot2,  
-	GSEABase, 
-	GSVA,
-	SingleCellExperiment,
-	ggridges,
-	msigdbr,
-	stats, 
-	BiocParallel, 
-	Matrix,
-	broom, 
-	reshape2, 
-	patchwork, 
-	MatrixGenerics,
-	utils,
-	rlang,
-	SummarizedExperiment,
-	UCell
+    AUCell,
+    grDevices,
+    dplyr,
+    ggdist,
+    ggplot2,
+    ggpointdensity,
+    GSEABase,
+    GSVA (>= 1.51.5),
+    SingleCellExperiment,
+    ggridges,
+    msigdbr,
+    stats,
+    reshape2,
+    patchwork,
+    MatrixGenerics,
+    utils,
+    SummarizedExperiment,
+    UCell,
+    stringr,
+    methods,
+    SeuratObject
 Suggests: 
-	Seurat,
-	SeuratObject,
-	knitr, 
-	rmarkdown,
-	markdown, 
-	BiocStyle,
-	testthat,
-	dittoSeq (>= 1.1.2)
+    Seurat,
+    scran,
+    knitr,
+    rmarkdown,
+    markdown,
+    BiocStyle,
+    RColorBrewer,
+    rlang,
+    spelling,
+    testthat (>= 3.0.0),
+    vdiffr
 VignetteBuilder: knitr
+Language: en-US

LICENSE

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+MIT License
+
+Copyright (c) 2023 Nick Borcherding
+
+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.