diff --git a/.github/workflows/render-README.yaml b/.github/workflows/render-README.yaml index 6f09d61..36f59f1 100644 --- a/.github/workflows/render-README.yaml +++ b/.github/workflows/render-README.yaml @@ -4,7 +4,7 @@ on: push: branches: main - paths: README.Rmd + paths: [README.Rmd, render-README.yaml] name: render-README @@ -22,11 +22,11 @@ jobs: - uses: r-lib/actions/setup-pandoc@v2 - name: install CRAN packages - run: Rscript -e 'install.packages(c("rmarkdown","ggplot2", "dplyr", "purrr", "remotes", "BiocManager"))' + run: Rscript -e 'install.packages(c("rmarkdown","ggplot2", "dplyr", "purrr", "remotes", "caret", "BiocManager"))' - name: install BioConductor packages run: Rscript -e 'BiocManager::install(c("SingleCellExperiment", "scater", "scran"))' - name: install GitHub packages - run: Rscript -e 'remotes::install_github("jr-leary7/scLANE"); remotes::install_github("rhondabacher/scaffold")' + run: Rscript -e 'remotes::install_github("jr-leary7/scLANE")' - name: render README run: Rscript -e 'rmarkdown::render("README.Rmd", output_format = "md_document")' - name: commit rendered README diff --git a/README.Rmd b/README.Rmd index 1ade39b..5cb67d2 100644 --- a/README.Rmd +++ b/README.Rmd @@ -68,7 +68,7 @@ filter <- dplyr::filter We read a previously-simulated dataset comprised of cells from 3 subjects exhibiting a homogeneous trajectory structure from [the Zenodo repository](https://doi.org/10.5281/zenodo.8433077). The underlying true pseudotime values are stored in the `colData` slot of the `SingleCellExperiment` object under the name **cell_time_normed**. ```{r sim, results='hide'} -sim_data <- readRDS(url("https://zenodo.org/record/8433077/files/scLANE_sim_data.Rds")) +sim_data <- readRDS(url("https://zenodo.org/records/8433077/files/scLANE_sim_data.Rds")) ``` The PCA embeddings show us a pretty simple trajectory that's strongly correlated with the first principal component.