Initial commit recall (compared to callback, adds various null distri…

…butions, renames method

.Rbuildignore

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+^LICENSE\.md$
+^Dockerfile$
+^tmp$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

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+*.html

.github/workflows/check-standard.yml

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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@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

.github/workflows/docker-image.yml

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+name: Docker Image CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Build the Docker image
+      run: docker build . --file Dockerfile --tag recall:$(date +%s)

.github/workflows/pkgdown.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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/super-linter.yml

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+# This workflow executes several linters on changed files based on languages used in your code base whenever
+# you push a code or open a pull request.
+#
+# You can adjust the behavior by modifying this file.
+# For more information, see:
+# https://github.com/github/super-linter
+name: Lint Code Base
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+jobs:
+  run-lint:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          # Full git history is needed to get a proper list of changed files within `super-linter`
+          fetch-depth: 0
+
+      - name: Lint Code Base
+        uses: github/super-linter@v4
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: "main"
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/
+.Rproj.user
+.Rdata
+.DS_Store
+docs
+inst/doc

DESCRIPTION

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+Package: recall
+Title: Calibrated clustering with artificial variables to avoid over-clustering in single-cell RNA-sequencing
+Version: 0.0.0
+Authors@R: 
+    person("Alan", "DenAdel", , "alan_denadel@brown.edu", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-7985-6789"))
+Description: recall (Calibrated Clustering with Artificial Variables) is a method for protecting
+ against over-clustering by controlling for the impact of double-dipping. The approach 
+    can be applied to any clustering algorithm (implemented are the Louvain and Leiden algorithms with
+    plans forK-means, and hierarchical clustering algorithms). The method provides state-of-the-art
+    clustering performance and can rapidly analyze large-scale scRNA-seq studies and is 
+    compatible with the Seurat library.
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+Imports: 
+    Matrix,
+    Seurat (>= 5.0.1),
+    SingleCellExperiment,
+    scDesign3,
+    SummarizedExperiment,
+    MASS,
+    fitdistrplus,
+    lamW,
+    knockoff,
+    future,
+    stats,
+    cli,
+    stringr,
+    countsplit
+License: MIT + file LICENSE
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr
+URL: https://lcrawlab.github.io/recall/

Dockerfile

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+FROM rocker/verse:4.0.5
+
+RUN R -e "install.packages('.', type = 'source', repos = NULL)"

LICENSE

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+YEAR: 2024
+COPYRIGHT HOLDER: recall authors

LICENSE.md

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+# MIT License
+
+Copyright (c) 2024 recall 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

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+# Generated by roxygen2: do not edit by hand
+
+export(FindClustersCallback)
+export(FindClustersCountsplit)
+export(seurat_workflow)

R/copula.R

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+simulate_data_scDesign3 <- function(data_matrix, cores, family) {
+    sce <- SingleCellExperiment::SingleCellExperiment(list(counts = data_matrix))
+    SummarizedExperiment::colData(sce)$cell_type <- "1" # scDesign3 needs a cell type so we just make it the same for all cells
+
+    simulated_data <- scDesign3::scdesign3(sce,
+                                           celltype = "cell_type",
+                                           pseudotime = NULL,
+                                           spatial = NULL,
+                                           other_covariates = NULL,
+                                           empirical_quantile = FALSE,
+                                           usebam=TRUE, # to speedup marginal inference
+                                           mu_formula = "1",
+                                           sigma_formula = "1",
+                                           corr_formula = "1",
+                                           family_use = family, # this is the key parameter
+                                           nonzerovar = FALSE,
+                                           n_cores = cores,
+                                           parallelization = "mcmapply",
+                                           important_feature = "all",
+                                           nonnegative = FALSE,
+                                           copula = "gaussian",
+                                           fastmvn = TRUE)
+
+    ko <- simulated_data$new_count
+
+    return(ko)
+}
+
+
+#' @title todo
+#'
+#' @description Given data, computes todo
+#'
+#' @param data_matrix The data to estimate parameters from.
+#' @param cores The number of CPU cores to use in estimation by scDesign3.
+#' @returns todo
+#' @name estimate_negative_binomial_copula
+estimate_zi_poisson_copula <- function(data_matrix, cores) {
+    family <- "zip"
+    ko <- simulate_data_scDesign3(data_matrix, cores, family)
+    return(ko)
+}
+
+
+#' @title todo
+#'
+#' @description Given data, computes todo
+#'
+#' @param data_matrix The data to estimate parameters from.
+#' @param cores The number of CPU cores to use in estimation by scDesign3.
+#' @returns todo
+#' @name estimate_negative_binomial_copula
+estimate_negative_binomial_copula <- function(data_matrix, cores) {
+    family <- "nb"
+    ko <- simulate_data_scDesign3(data_matrix, cores, family)
+    return(ko)
+}
+
+
+#' @title todo
+#'
+#' @description Given data, computes todo
+#'
+#' @param data_matrix The data to estimate parameters from.
+#' @param cores The number of CPU cores to use in estimation by scDesign3.
+#' @returns todo
+#' @name estimate_negative_binomial_copula
+estimate_poisson_copula <- function(data_matrix, cores) {
+    family <- "poisson"
+    ko <- simulate_data_scDesign3(data_matrix, cores, family)
+    return(ko)
+}
+
+
+
+
+#' @title todo
+#'
+#' @description Given data, computes todo
+#'
+#' @param data_matrix The data to estimate parameters from.
+#' @param cores The number of CPU cores to use in estimation by scDesign3.
+#' @returns todo
+#' @name estimate_negative_binomial_copula
+estimate_gaussian_copula <- function(data_matrix, cores) {
+    family <- "gaussian"
+    ko <- simulate_data_scDesign3(data_matrix, cores, family)
+    return(ko)
+}
+
+
+