diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 60c89c0..e384fd7 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -4,9 +4,10 @@ on: push: branches: [main, master] pull_request: - branches: [main, master] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: @@ -29,7 +30,7 @@ jobs: R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v5 - uses: r-lib/actions/setup-pandoc@v2 @@ -39,10 +40,6 @@ jobs: http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - - uses: actions/setup-python@v4 - with: - python-version: '3.10' - - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: any::rcmdcheck @@ -57,3 +54,4 @@ jobs: - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml deleted file mode 100644 index 2c5bb50..0000000 --- a/.github/workflows/test-coverage.yaml +++ /dev/null @@ -1,50 +0,0 @@ -# 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(Sys.getenv("RUNNER_TEMP"), "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 diff --git a/DESCRIPTION b/DESCRIPTION index fbf9d96..fcc7fbf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: SCORPIUS Type: Package Title: Inferring Developmental Chronologies from Single-Cell RNA Sequencing Data -Version: 1.0.9 +Version: 1.0.10 Description: An accurate and easy tool for performing linear trajectory inference on single cells using single-cell RNA sequencing data. In addition, 'SCORPIUS' provides functions for discovering the most important genes with respect to @@ -12,13 +12,13 @@ Authors@R: c( "Robrecht", "Cannoodt", email = "rcannood@gmail.com", role = c("aut", "cre"), - comment = c(ORCID = "0000-0003-3641-729X", github = "rcannood") + comment = c(ORCID = "0000-0003-3641-729X") ), person( "Wouter", "Saelens", email = "wouter.saelens@ugent.be", role = c("ctb"), - comment = c(ORCID = "0000-0002-7114-6248", github = "zouter") + comment = c(ORCID = "0000-0002-7114-6248") ) ) License: GPL-3 @@ -28,7 +28,7 @@ URL: https://github.com/rcannood/SCORPIUS, http://rcannood.github.io/SCORPIUS/ BugReports: https://github.com/rcannood/SCORPIUS/issues LazyData: true -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.3 VignetteBuilder: knitr Depends: diff --git a/NEWS.md b/NEWS.md index c47f8ed..e408550 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# SCORPIUS 1.0.10 + +* Fix documentation issues (PR #47). + # SCORPIUS 1.0.9 * Resubmission after babelwhale was removed from CRAN. diff --git a/R/dimensionality_reduction.R b/R/dimensionality_reduction.R index 62efd0d..62490a5 100644 --- a/R/dimensionality_reduction.R +++ b/R/dimensionality_reduction.R @@ -5,7 +5,7 @@ #' #' @param x a numeric matrix #' @param dist the distance metric to be used; can be any of the metrics listed in [dynutils::calculate_distance()]. -#' @param ndim the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}. +#' @param ndim the maximum dimension of the space which the data are to be represented in; must be in \eqn{[1, n - 1]}, with \eqn{n} the number of samples (rows) in \code{x}. #' @param num_landmarks the number of landmarks to be selected. #' #' @return A matrix containing the coordinates of each sample, represented in an \code{ndim}-dimensional space. diff --git a/R/package.R b/R/package.R index 7c37eb4..ee1884e 100644 --- a/R/package.R +++ b/R/package.R @@ -3,7 +3,6 @@ #' SCORPIUS orders single cells with regard to an implicit timeline, #' such as cellular development or progression over time. #' -#' @docType package #' @name SCORPIUS-package #' @aliases SCORPIUS-package SCORPIUS #' @@ -43,4 +42,4 @@ #' path = traj$path, #' progression_group = ginhoux$sample_info$group_name #' ) -NULL +"_PACKAGE" diff --git a/README.Rmd b/README.Rmd index 45b7ccc..d3952e5 100644 --- a/README.Rmd +++ b/README.Rmd @@ -20,7 +20,6 @@ library(tidyverse) [![R-CMD-check](https://github.com/rcannood/SCORPIUS/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rcannood/SCORPIUS/actions/workflows/R-CMD-check.yaml) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/SCORPIUS)](https://cran.r-project.org/package=SCORPIUS) -[![Codecov test coverage](https://codecov.io/gh/rcannood/SCORPIUS/branch/master/graph/badge.svg)](https://app.codecov.io/gh/rcannood/SCORPIUS?branch=master) SCORPIUS an unsupervised approach for inferring linear developmental chronologies from single-cell diff --git a/README.md b/README.md index 61c8e0a..6ed506c 100644 --- a/README.md +++ b/README.md @@ -5,8 +5,6 @@ [![R-CMD-check](https://github.com/rcannood/SCORPIUS/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rcannood/SCORPIUS/actions/workflows/R-CMD-check.yaml) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/SCORPIUS)](https://cran.r-project.org/package=SCORPIUS) -[![Codecov test -coverage](https://codecov.io/gh/rcannood/SCORPIUS/branch/master/graph/badge.svg)](https://app.codecov.io/gh/rcannood/SCORPIUS?branch=master) SCORPIUS an unsupervised approach for inferring linear developmental diff --git a/cran-comments.md b/cran-comments.md index fa945b3..9b9897f 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,19 +1,18 @@ -# SCORPIUS 1.0.9 +# SCORPIUS 1.0.10 -* Resubmission after babelwhale was removed from CRAN. +* Fix documentation issues (PR #47). -* DOCUMENTATION: Add vignette for working with AnnData objects. - -* DOCUMENTATION: Add vignette for working with SingleCellExperiment objects. - -* DOCUMENTATION: Create pkgdown site. +# Checks -* DOCUMENTATION: Update citEntry to bibentry. +## R CMD check results -* DOCUMENTATION: Reduce execution time of examples by downscaling the example dataset. + * checking whether package ‘SCORPIUS’ can be installed ... WARNING + Warning: Found the following significant warnings: + Warning: `invoke()` was deprecated in purrr 1.0.0. + See ‘/home/runner/work/SCORPIUS/SCORPIUS/check/SCORPIUS.Rcheck/00install.out’ for details. -# Checks + 0 errors ✔ | 1 warning ✖ | 0 notes ✔ -## R CMD check results +This is a WARNING caused by dynwrap <= 1.2.4. -0 errors | 0 warnings | 0 notes \ No newline at end of file +dynwrap 1.2.5 has been accepted for release on CRAN, some warnings may still appear until all builds are available on CRAN. diff --git a/man/SCORPIUS-package.Rd b/man/SCORPIUS-package.Rd index 0e8254c..1a08c7c 100644 --- a/man/SCORPIUS-package.Rd +++ b/man/SCORPIUS-package.Rd @@ -49,3 +49,21 @@ Cannoodt R. et al., SCORPIUS improves trajectory inference and identifies novel bioRxiv (Oct., 2016). \doi{10.1101/079509} (\href{https://www.biorxiv.org/content/biorxiv/early/2016/10/07/079509.full.pdf}{PDF}). } +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/rcannood/SCORPIUS} + \item \url{http://rcannood.github.io/SCORPIUS/} + \item Report bugs at \url{https://github.com/rcannood/SCORPIUS/issues} +} + +} +\author{ +\strong{Maintainer}: Robrecht Cannoodt \email{rcannood@gmail.com} (\href{https://orcid.org/0000-0003-3641-729X}{ORCID}) + +Other contributors: +\itemize{ + \item Wouter Saelens \email{wouter.saelens@ugent.be} (\href{https://orcid.org/0000-0002-7114-6248}{ORCID}) [contributor] +} + +} diff --git a/man/reduce_dimensionality.Rd b/man/reduce_dimensionality.Rd index f08c839..723fb95 100644 --- a/man/reduce_dimensionality.Rd +++ b/man/reduce_dimensionality.Rd @@ -16,7 +16,7 @@ reduce_dimensionality( \item{dist}{the distance metric to be used; can be any of the metrics listed in \code{\link[dynutils:calculate_distance]{dynutils::calculate_distance()}}.} -\item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.} +\item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in \eqn{[1, n - 1]}, with \eqn{n} the number of samples (rows) in \code{x}.} \item{num_landmarks}{the number of landmarks to be selected.} } diff --git a/man/ti_scorpius.Rd b/man/ti_scorpius.Rd index 85b67b6..e2dfd62 100644 --- a/man/ti_scorpius.Rd +++ b/man/ti_scorpius.Rd @@ -15,7 +15,7 @@ ti_scorpius( ) } \arguments{ -\item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}. Default: spearman. Format: character.} +\item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: \{spearman, pearson, cosine\}. Default: spearman. Format: character.} \item{ndim}{The number of dimensions in the new space. Domain: U(2, 20). Default: 3. Format: integer.} @@ -27,7 +27,7 @@ ti_scorpius( \item{stretch}{\code{principal_curve} parameter; a factor by which the curve can be extrapolated when points are projected. Domain: U(0, 5). Default: 0. Format: numeric.} -\item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.} +\item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: \{smooth_spline, lowess, periodic_lowess\}. Default: smooth_spline. Format: character.} } \value{ A dynwrap TI method. diff --git a/vignettes/seurat.Rmd b/vignettes/seurat.Rmd index f346dea..1c5fb68 100644 --- a/vignettes/seurat.Rmd +++ b/vignettes/seurat.Rmd @@ -43,7 +43,7 @@ srt <- NormalizeData(srt) Fetch the expression data from the Seurat object as follows. ```{r fetchdata} -expression <- t(srt@assays$RNA@data) +expression <- t(as.matrix(LayerData(srt, assay = "RNA", layer = "data"))) ``` Also fetch some metadata from the Seurat object. Change `group_name` to whatever column in `srt@meta.data` you are interested in.