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Katsevich-Lab · Jan 30, 2025 · ef052ab · ef052ab
2 parents 52b14c7 + 082a104
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diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml
@@ -0,0 +1,64 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: ['*']  # Run CI on all branches to allow pre-PR testing
+  pull_request:
+    branches: [main, dev]
+
+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: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install system dependencies
+        run: |
+          if [[ "$RUNNER_OS" == "Linux" ]]; then
+            sudo apt-get update
+            sudo apt-get install -y build-essential libhdf5-dev libcurl4-openssl-dev libxml2-dev libssl-dev
+          elif [[ "$RUNNER_OS" == "macOS" ]]; then
+            brew update
+            brew install hdf5 curl libxml2 openssl
+            echo 'export PATH="/usr/local/opt/openssl/bin:$PATH"' >> ~/.zshrc
+          else
+            echo "Unsupported OS: $RUNNER_OS"
+            exit 1
+          fi
+
+      - 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
+
+      - name: Install ondisc R package (macOS only)
+        if: ${{ matrix.config.os == 'macOS-latest' }}
+        run: |
+          Rscript -e "if (!requireNamespace('remotes', quietly = TRUE)) install.packages('remotes')"
+          Rscript -e "remotes::install_github('timothy-barry/ondisc')"
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v2
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: sceptre
 Title: Analysis of Single-Cell CRISPR Screen Data
-Version: 0.10.0
+Version: 0.10.2
 Authors@R: 
     c(person(given = "Timothy",
            family = "Barry",
@@ -39,15 +39,15 @@ Depends:
     R (>= 4.1)
 Suggests:
     ondisc,
+    R.utils,
     sessioninfo,
-    sceptredata,
     rmarkdown,
     knitr,
     parallel,
     testthat (>= 3.0.0),
     magrittr,
     MASS
-Remotes: github::timothy-barry/ondisc, github::katsevich-lab/sceptredata
+Remotes: github::timothy-barry/ondisc
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 URL: https://timothy-barry.github.io/sceptre-book/, https://github.com/Katsevich-Lab/sceptre

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+# sceptre 0.10.2 (2025-01-17)
+
+Version 0.10.2 is a minor update in which we replaced the larger, real example
+data by smaller, simulated example data. Furthermore, the example data now live 
+in the `sceptre` package, rather than in the external `sceptredata` package. 
+Finally, the R-CMD-CHECK badge was restored on the website.
+
+# sceptre 0.10.1 (2024-04-30)
+
+Version 0.10.1 includes minor updates to v0.10.0. A new gene position data frame 
+`gene_position_data_frame_grch37` was added.
+
 # sceptre 0.10.0 (2024-04-02)
 
 Version 0.10.0 is a major update to the `sceptre` package. This version provides support for the analysis of large-scale single-cell CRISPR screen data. It also includes several other, minor updates.

diff --git a/R/data.R b/R/data.R
@@ -11,3 +11,43 @@
 #' @rdname gene_position_data_frame_grch38
 #' @usage data(gene_position_data_frame_grch37)
 "gene_position_data_frame_grch37"
+
+#' Example high-MOI data
+#'
+#' The example high-MOI CRISPRi data are a small simulated dataset modeled on
+#' that of "A genome-wide framework for mapping gene regulation via cellular
+#' genetic screens" by Gasperini et al., 2019. These data contain perturbations
+#' both of gene transcription start sites (TSSs) and enhancers, as well as non-
+#' targeting perturbations.
+#'
+#' The example data are stored in a list containing the following components:
+#' - `response_matrix`: the gene-by-cell expression matrix
+#' - `grna_matrix`: the gRNA-by-cell expression matrix
+#' - `extra_covariates`: a data frame containing a single column, `batch`, specifying the batch in which each cell was sequenced (`batch_1` or `batch_2`)
+#' - `gene_names`: the human-readable name of each gene
+#'
+#' @usage data(highmoi_example_data)
+"highmoi_example_data"
+
+#' gRNA target data frame
+#'
+#' The gRNA target data frame corresponding to the example high MOI data. The data frame contains the columns `grna_id` (ID of an individual gRNA), `grna_target` (genomic target of the gRNA), `chr` (target chromosome), `start` (start coordinate of target location), and `end` (end coordinate of target location).
+#' @usage data(grna_target_data_frame_highmoi)
+"grna_target_data_frame_highmoi"
+
+#' Example low-MOI data
+#'
+#' The example low-MOI data are a small simulated dataset modeled on that in the
+#' paper "Characterizing the molecular regulation of inhibitory immune
+#' checkpoints with multimodal single-cell screens" by Papalexi et al., 2021.
+#' This dataset includes gene-targeting CRISPRko perturbations as well as non-
+#' targeting perturbations.
+#'
+#' The example data are stored in a list containing four components:
+#' - `response_matrix`: the gene-by-cell expression matrix
+#' - `grna_matrix`: the gRNA-by-cell expression matrix
+#' - `grna_target_data_frame`:  a data frame containing the columns `grna_id` (ID of an individual gRNA) and `grna_target` (genomic target of the gRNA)
+#' - `extra_covariates`: a data frame with a single column, `batch`, specifying the batch in which each cell was sequenced (`batch_1` or `batch_2`)
+#'
+#' @usage data(lowmoi_example_data)
+"lowmoi_example_data"
diff --git a/R/getters_and_setters.R b/R/getters_and_setters.R
@@ -13,7 +13,7 @@
 #' @export
 #' @examples
 #' # 1. create a sceptre_object
-#' library(sceptredata)
+#'
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' sceptre_object <- import_data(
@@ -62,7 +62,6 @@ get_cell_covariates <- function(sceptre_object) {
 #' @return a sparse logical matrix containing the gRNA-to-cell assignments
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data

diff --git a/R/import_functs.R b/R/import_functs.R
@@ -17,7 +17,6 @@
 #' @return an initialized `sceptre_object`
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data("lowmoi_example_data")
 #' # 1. initialize a standard sceptre_object from R objects
 #' sceptre_object <- import_data(
@@ -142,10 +141,9 @@ import_data_use_ondisc <- function(response_matrix, grna_matrix, grna_target_dat
 #' @return an initialized `sceptre_object`
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(grna_target_data_frame_highmoi)
 #' directories <- paste0(
-#'   system.file("extdata", package = "sceptredata"),
+#'   system.file("extdata", package = "sceptre"),
 #'   "/highmoi_example/gem_group_", c(1, 2)
 #' )
 #'
@@ -372,7 +370,7 @@ import_data_from_cellranger_use_ondisc <- function(directories, moi, grna_target
 #'
 #' @examples
 #' directory <- paste0(
-#'   system.file("extdata", package = "sceptredata"),
+#'   system.file("extdata", package = "sceptre"),
 #'   "/parse_example/"
 #' )
 #' gene_mat_fp <- paste0(directory, "gene_mat.mtx")

diff --git a/R/ondisc_functs.R b/R/ondisc_functs.R
@@ -14,7 +14,6 @@
 #' @return `write_ondisc_backed_sceptre_object()` returns NULL, and `read_ondisc_backed_sceptre_object()` returns an `ondisc`-backed `sceptre_object`
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(lowmoi_example_data)
 #' # 1. create ondisc-backed sceptre_object
 #' sceptre_object <- import_data(

diff --git a/R/pair_constructor_functs.R b/R/pair_constructor_functs.R
@@ -10,7 +10,6 @@
 #' @return a data frame with columns `grna_target` and `response_id` containing the *cis* pairs
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -91,7 +90,6 @@ construct_cis_pairs <- function(sceptre_object, positive_control_pairs = data.fr
 #' @return a data frame with columns `grna_target` and `response_id` containing the *trans* discovery set
 #' @export
 #' @examples
-#' library(sceptredata)
 #' # 1. low-moi, gene-targeting screen
 #' data("lowmoi_example_data")
 #' sceptre_object <- import_data(
@@ -158,7 +156,6 @@ construct_trans_pairs <- function(sceptre_object, positive_control_pairs = data.
 #' @return a data frame with columns `grna_target` and `response_id` containing the positive control pairs
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data

diff --git a/R/plotting_functions.R b/R/plotting_functions.R
@@ -27,7 +27,6 @@ get_my_theme <- function(element_text_size = 11) {
 #' @return a single \code{ggplot2} plot
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' import_data(
@@ -148,7 +147,6 @@ plot_grna_count_distributions <- function(sceptre_object, n_grnas_to_plot = 4L,
 #' @return a single \code{cowplot} object containing the combined panels (if \code{return_indiv_plots} is set to \code{TRUE}) or a list of the individual panels (if \code{return_indiv_plots} is set to \code{FALSE})
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' import_data(
@@ -298,7 +296,6 @@ plot_assign_grnas <- function(sceptre_object, n_grnas_to_plot = 3L, grnas_to_plo
 #' @export
 #'
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -496,7 +493,6 @@ make_volcano_plot <- function(discovery_result, p_thresh, x_limits = c(-1.5, 1.5
 #'
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -611,7 +607,6 @@ plot_run_discovery_analysis <- function(sceptre_object, x_limits = c(-1.5, 1.5),
 #' @return a single \code{cowplot} object containing the combined panels (if \code{return_indiv_plots} is set to \code{TRUE}) or a list of the individual panels (if \code{return_indiv_plots} is set to \code{FALSE})
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' import_data(
@@ -685,7 +680,6 @@ plot_covariates <- function(sceptre_object,
 #'
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -808,7 +802,6 @@ plot_pairwise_qc <- function(sceptre_object, downsample_pairs = 10000L, point_si
 #' @return a single \code{ggplot2} plot
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -904,7 +897,6 @@ downsample_result_data_frame <- function(result_df, downsample_pairs = 1000) {
 #' @return a violin plot
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -930,8 +922,8 @@ downsample_result_data_frame <- function(result_df, downsample_pairs = 1000) {
 #'     n_processors = 2
 #'   ) |>
 #'   plot_response_grna_target_pair(
-#'     response_id = "ENSG00000136938",
-#'     grna_target = "candidate_enh_20"
+#'     response_id = "ENSG00000211641",
+#'     grna_target = "candidate_enh_15"
 #'   )
 plot_response_grna_target_pair <- function(sceptre_object, response_id, grna_target) {
   # check that grnas have been assigned and qc has been called

diff --git a/R/s4_analysis_functs_1.R b/R/s4_analysis_functs_1.R
@@ -21,7 +21,6 @@
 #'
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -162,7 +161,6 @@ set_analysis_parameters <- function(sceptre_object,
 #' @return an updated `sceptre_object` in which the gRNA assignments have been carried out
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data("lowmoi_example_data")
 #' # 1. import data, set default analysis parameters
 #' sceptre_object <- import_data(
@@ -248,7 +246,6 @@ assign_grnas <- function(sceptre_object, method = "default", print_progress = TR
 #' @return an updated `sceptre_object` in which cellwise and pairwise QC have been applied
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data

diff --git a/R/s4_analysis_functs_2.R b/R/s4_analysis_functs_2.R
@@ -14,7 +14,6 @@
 #'
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -146,7 +145,6 @@ process_calibration_result <- function(result, sceptre_object) {
 #'
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -227,7 +225,6 @@ run_power_check <- function(sceptre_object, output_amount = 1, print_progress =
 #'
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -512,7 +509,6 @@ add_num_cells_to_result <- function(result, sceptre_object, is_calibration_check
 #' @returns a data frame containing the results of the analysis
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -560,7 +556,6 @@ get_result <- function(sceptre_object, analysis) {
 #' @return the value NULL
 #' @export
 #' @examples
-#' library(sceptredata)
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data

diff --git a/R/s4_helpers.R b/R/s4_helpers.R
@@ -41,7 +41,7 @@ setMethod("show", signature = signature("sceptre_object"), function(object) {
 #' @return the value NULL
 #' @export
 #' @examples
-#' library(sceptredata)
+#' 
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data
@@ -158,7 +158,7 @@ setMethod("print", signature = signature("sceptre_object"), function(x) {
 #'
 #' @export
 #' @examples
-#' library(sceptredata)
+#' 
 #' data(highmoi_example_data)
 #' data(grna_target_data_frame_highmoi)
 #' # import data