diff --git a/.github/workflows/docker_all-modules.yml b/.github/workflows/docker_all-modules.yml index 0f1a45fc0..a2285a0e0 100644 --- a/.github/workflows/docker_all-modules.yml +++ b/.github/workflows/docker_all-modules.yml @@ -39,6 +39,9 @@ jobs: - cell-type-ewings - doublet-detection - cell-type-wilms-tumor-06 + - cell-type-wilms-tumor-14 + - cell-type-nonETP-ALL-03 + - cell-type-ETP-ALL-03 uses: ./.github/workflows/build-push-docker-module.yml if: github.repository_owner == 'AlexsLemonade' with: diff --git a/.github/workflows/docker_cell-type-ETP-ALL-03.yml b/.github/workflows/docker_cell-type-ETP-ALL-03.yml new file mode 100644 index 000000000..f39b838ff --- /dev/null +++ b/.github/workflows/docker_cell-type-ETP-ALL-03.yml @@ -0,0 +1,63 @@ +# This is a workflow to build the docker image for the cell-type-ETP-ALL-03 module +# +# Docker modules are run on pull requests when code for files that affect the Docker image have changed. +# If other files are used during the Docker build, they should be added to `paths` +# +# At module initialization, this workflow is inactive, and needs to be activated manually + +name: Build docker image for cell-type-ETP-ALL-03 + +concurrency: + # only one run per branch at a time + group: "docker_cell-type-ETP-ALL-03_${{ github.ref }}" + cancel-in-progress: true + +on: + pull_request: + branches: + - main + paths: + - "analyses/cell-type-ETP-ALL-03/Dockerfile" + - "analyses/cell-type-ETP-ALL-03/.dockerignore" + - "analyses/cell-type-ETP-ALL-03/renv.lock" + - "analyses/cell-type-ETP-ALL-03/conda-lock.yml" + push: + branches: + - main + paths: + - "analyses/cell-type-ETP-ALL-03/Dockerfile" + - "analyses/cell-type-ETP-ALL-03/.dockerignore" + - "analyses/cell-type-ETP-ALL-03/renv.lock" + - "analyses/cell-type-ETP-ALL-03/conda-lock.yml" + workflow_dispatch: + inputs: + push-ecr: + description: "Push to AWS ECR" + type: boolean + required: true + +jobs: + test-build: + name: Test Build Docker Image + if: github.event_name == 'pull_request' || (contains(github.event_name, 'workflow_') && !inputs.push-ecr) + runs-on: ubuntu-latest + + steps: + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + + - name: Build image + uses: docker/build-push-action@v5 + with: + context: "{{defaultContext}}:analyses/cell-type-ETP-ALL-03" + push: false + cache-from: type=gha + cache-to: type=gha,mode=max + + build-push: + name: Build and Push Docker Image + if: github.repository_owner == 'AlexsLemonade' && (github.event_name == 'push' || inputs.push-ecr) + uses: ./.github/workflows/build-push-docker-module.yml + with: + module: "cell-type-ETP-ALL-03" + push-ecr: true diff --git a/.github/workflows/run_all-modules.yml b/.github/workflows/run_all-modules.yml index fc6885e50..2224fe81f 100644 --- a/.github/workflows/run_all-modules.yml +++ b/.github/workflows/run_all-modules.yml @@ -34,7 +34,13 @@ jobs: cell-type-wilms-14: uses: ./.github/workflows/run_cell-type-wilms-tumor-14.yml - ## Add additional modules above this comment, and to the needs list below + cell-type-ETP-ALL-03: + uses: ./.github/workflows/run_cell-type-ETP-ALL-03.yml + + cell-type-nonETP-ALL-03: + uses: ./.github/workflows/run_cell-type-nonETP-ALL-03.yml + + ## Add additional modules above this comment, and to the needs list below check-jobs: if: ${{ always() }} needs: @@ -42,6 +48,10 @@ jobs: - hello-python - doublet-detection - cell-type-ewings + - cell-type-wilms-06 + - cell-type-wilms-14 + - cell-type-ETP-ALL-03 + - cell-type-nonETP-ALL-03 runs-on: ubuntu-latest steps: - name: Checkout template file diff --git a/.github/workflows/run_cell-type-ETP-ALL-03.yml b/.github/workflows/run_cell-type-ETP-ALL-03.yml new file mode 100644 index 000000000..1ad55dcbc --- /dev/null +++ b/.github/workflows/run_cell-type-ETP-ALL-03.yml @@ -0,0 +1,92 @@ +# This is a workflow to run the cell-type-ETP-ALL-03 module +# +# Analysis modules are run based on three triggers: +# - Manual trigger +# - On pull requests where code in the module has changed +# - As a reusable workflow called from a separate workflow which periodically runs all modules +# +# At initialization, only the manual trigger is active + +name: Run cell-type-ETP-ALL-03 analysis module +env: + MODULE_PATH: analyses/cell-type-ETP-ALL-03 + AWS_DEFAULT_REGION: us-east-2 + +concurrency: + # only one run per branch at a time + group: "run_cell-type-ETP-ALL-03_${{ github.ref }}" + cancel-in-progress: true + +on: + workflow_dispatch: + workflow_call: + pull_request: + branches: + - main + paths: + - analyses/cell-type-ETP-ALL-03/** + - "!analyses/cell-type-ETP-ALL-03/Dockerfile" + - "!analyses/cell-type-ETP-ALL-03/.dockerignore" + - .github/workflows/run_cell-type-ETP-ALL-03.yml + +jobs: + run-module: + if: github.repository_owner == 'AlexsLemonade' + runs-on: ubuntu-latest + defaults: + run: + shell: bash -el {0} + + steps: + - name: Checkout repo + uses: actions/checkout@v4 + + - name: Set up R + uses: r-lib/actions/setup-r@v2 + with: + r-version: 4.4.0 + use-public-rspm: true + + - name: Set up pandoc + uses: r-lib/actions/setup-pandoc@v2 + + - name: Install system dependencies + run: | + sudo apt-get install -y libcurl4-openssl-dev \ + libhdf5-dev \ + libglpk40 \ + libxml2-dev \ + libfontconfig1-dev \ + libharfbuzz-dev \ + libfribidi-dev \ + libtiff5-dev + + - name: Set up renv + uses: r-lib/actions/setup-renv@v2 + with: + working-directory: ${{ env.MODULE_PATH }} + + - name: Set up conda + # Note that this creates and activates an environment named 'test' by default + uses: conda-incubator/setup-miniconda@v3 + with: + miniforge-version: latest + + - name: Install conda-lock and activate locked conda environment + run: | + conda install conda-lock + conda-lock install --name openscpca-cell-type-ETP-ALL-03 ${MODULE_PATH}/conda-lock.yml + + # Update this step as needed to download the desired data + - name: Download test data + run: | + ./download-data.py --projects SCPCP000003 --test-data --format SCE + ./download-results.py --projects SCPCP000003 --test-data --modules doublet-detection + + - name: Run analysis module + run: | + cd ${MODULE_PATH} + # run module script(s) here + Rscript scripts/00-01_processing_rds.R + Rscript scripts/02-03_annotation.R + Rscript scripts/multipanel_plot.R diff --git a/analyses/cell-type-ETP-ALL-03/.Rprofile b/analyses/cell-type-ETP-ALL-03/.Rprofile new file mode 100644 index 000000000..7eae9e102 --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/.Rprofile @@ -0,0 +1,4 @@ +# Don't activate renv in an OpenScPCA docker image +if (Sys.getenv('OPENSCPCA_DOCKER') != 'TRUE') { + source('renv/activate.R') +} diff --git a/analyses/cell-type-ETP-ALL-03/.dockerignore b/analyses/cell-type-ETP-ALL-03/.dockerignore new file mode 100644 index 000000000..23c79ccae --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/.dockerignore @@ -0,0 +1,8 @@ +# Ignore everything by default +* + +# Include specific files in the docker environment +!/renv.lock +!/requirements.txt +!/environment.yml +!/conda-lock.yml diff --git a/analyses/cell-type-ETP-ALL-03/.gitignore b/analyses/cell-type-ETP-ALL-03/.gitignore new file mode 100644 index 000000000..418755f52 --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/.gitignore @@ -0,0 +1,7 @@ +# Results should not be committed +/results/* +!/results/README.md + +# Ignore the scratch directory (but keep it present) +/scratch/* +!/scratch/.gitkeep diff --git a/analyses/cell-type-ETP-ALL-03/Azimuth_BM_level1.csv b/analyses/cell-type-ETP-ALL-03/Azimuth_BM_level1.csv new file mode 100644 index 000000000..c31f31785 --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/Azimuth_BM_level1.csv @@ -0,0 +1,18 @@ +tissueType,cellName,ensembl_id_positive_marker,ensembl_id_negative_marker,fullName,ontologyID +Immune system,B,"ENSG00000163534,ENSG00000132704,ENSG00000012124,ENSG00000138639,ENSG00000153064,ENSG00000156738,ENSG00000116191,ENSG00000104894,ENSG00000133789,ENSG00000105369",,B cell,CL_0000945 +Immune system,CD4 T,"ENSG00000172005,ENSG00000138795,ENSG00000168685,ENSG00000081059,ENSG00000227507,ENSG00000104660,ENSG00000198851,ENSG00000167286,ENSG00000160654,ENSG00000139193",,CD4 T cell,CL_0000624 +Immune system,CD8 T,"ENSG00000172116,ENSG00000153563,ENSG00000184613,ENSG00000167286,ENSG00000198851,ENSG00000160307,ENSG00000100450,ENSG00000160654,ENSG00000227191,ENSG00000271503",,CD8 T cell,CL_0000625 +Immune system,DC,"ENSG00000198178,ENSG00000115718,ENSG00000070031,ENSG00000169432,ENSG00000105251,ENSG00000155367,ENSG00000168913,ENSG00000132514,ENSG00000239961,ENSG00000163687",,Dendritic cell,CL_0000451 +Immune system,HSPC,"ENSG00000172995,ENSG00000186710,ENSG00000101200,ENSG00000163554,ENSG00000119888,ENSG00000188672,ENSG00000131016,ENSG00000112077,ENSG00000172247,ENSG00000170891",,Hematopoietic stem and progenitor cell,CL_0000037 +Immune system,Mono,"ENSG00000197353,ENSG00000110203,ENSG00000166523,ENSG00000104974,ENSG00000158825,ENSG00000162444,ENSG00000186074,ENSG00000171051,ENSG00000125810,ENSG00000014914",,Monocytes,CL_0000576 +Immune system,NK,"ENSG00000189430,ENSG00000198574,ENSG00000134545,ENSG00000150687,ENSG00000117281,ENSG00000156966,ENSG00000100385,ENSG00000115607,ENSG00000143184,ENSG00000150045",,Natural killer cell,CL_0000814 +Immune system,Other T,"ENSG00000144290,ENSG00000111796,ENSG00000168685,ENSG00000215788,ENSG00000069667,ENSG00000107742,ENSG00000178573,ENSG00000113088,ENSG00000152518,ENSG00000145220",,Other T cell,CL_0000084 +Immune system,Macrophage,"ENSG00000166211,ENSG00000121769,ENSG00000073754,ENSG00000275385,ENSG00000159189,ENSG00000173369,ENSG00000170323,ENSG00000173372,ENSG00000130203,ENSG00000250722",,Macrophage,CL_0000235 +Immune system,Early Eryth,"ENSG00000119865,ENSG00000179348,ENSG00000005961,ENSG00000106327,ENSG00000102145,ENSG00000105610,ENSG00000170891,ENSG00000135525,ENSG00000075618,ENSG00000130208",,Early Erythrocyte,CL_0000764 +Immune system,Late Eryth,"ENSG00000196188,ENSG00000112212,ENSG00000204010,ENSG00000188672,ENSG00000112077,ENSG00000163554,ENSG00000075340,ENSG00000119888,ENSG00000213934",,Late Erythrocyte,CL_0000764 +Immune system,Plasma,"ENSG00000115884,ENSG00000222037,ENSG00000211640,ENSG00000048462,ENSG00000211673,ENSG00000240505,ENSG00000211685,ENSG00000167476,ENSG00000143297,ENSG00000243466",,Plasma cell,CL_0000786 +Immune system,Platelet,"ENSG00000150681,ENSG00000187699,ENSG00000088726,ENSG00000169704,ENSG00000163737,ENSG00000163736,ENSG00000153071,ENSG00000113140,ENSG00000176783,ENSG00000124491",,Platelet,CL_0000233 +Immune system,Stromal,"ENSG00000115461,ENSG00000047457,ENSG00000091513,ENSG00000011465,ENSG00000139329,ENSG00000164692,ENSG00000147571,ENSG00000041982,ENSG00000152583,ENSG00000112175",,Stromal cell,CL_0000499 +Immune system,Blast,"ENSG00000002586,ENSG00000173762,ENSG00000124766,ENSG00000177606,ENSG00000117632,ENSG00000123416,ENSG00000167286",,Blast cell,CL_0000055 +Immune system,Cancer,"ENSG00000026508,ENSG00000119888,ENSG00000141736,ENSG00000086205,ENSG00000111057,ENSG00000007062",,Cancer cell,CL_0001064 +Immune system,Pre Eryth,"ENSG00000081237,ENSG00000170180,ENSG00000175792,ENSG00000072274,ENSG00000110195,ENSG00000135218,ENSG00000115232,ENSG00000244734,ENSG00000223609,ENSG00000133742",,Erythroid-like and erythroid precursor cell,CL_0000038 diff --git a/analyses/cell-type-ETP-ALL-03/Dockerfile b/analyses/cell-type-ETP-ALL-03/Dockerfile new file mode 100644 index 000000000..487d5fe68 --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/Dockerfile @@ -0,0 +1,64 @@ +FROM bioconductor/r-ver:3.19 + +# Labels following the Open Containers Initiative (OCI) recommendations +# For more information, see https://specs.opencontainers.org/image-spec/annotations/?v=v1.0.1 +LABEL org.opencontainers.image.title="openscpca/cell-type-ETP-ALL-03" +LABEL org.opencontainers.image.description="Docker image for the OpenScPCA analysis module 'cell-type-ETP-ALL-03'" +LABEL org.opencontainers.image.authors="OpenScPCA scpca@ccdatalab.org" +LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/analyses/cell-type-ETP-ALL-03" + +# Set an environment variable to allow checking if we are in an OpenScPCA container +ENV OPENSCPCA_DOCKER=TRUE + +# set a name for the conda environment +ARG ENV_NAME=openscpca-cell-type-ETP-ALL-03 + +# set environment variables to install conda +ENV PATH="/opt/conda/bin:${PATH}" + +# Install conda via miniforge +# adapted from https://github.com/conda-forge/miniforge-images/blob/master/ubuntu/Dockerfile +RUN curl -L "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -o /tmp/miniforge.sh \ + && bash /tmp/miniforge.sh -b -p /opt/conda \ + && rm -f /tmp/miniforge.sh \ + && conda clean --tarballs --index-cache --packages --yes \ + && find /opt/conda -follow -type f -name '*.a' -delete \ + && find /opt/conda -follow -type f -name '*.pyc' -delete \ + && conda clean --force-pkgs-dirs --all --yes + +# Activate conda environments in bash +RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh \ + && echo ". /opt/conda/etc/profile.d/conda.sh" >> /etc/skel/.bashrc \ + && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc + +# Install conda-lock +RUN conda install --channel=conda-forge --name=base conda-lock \ + && conda clean --all --yes + +# Install renv +RUN Rscript -e "install.packages('renv')" + +# Disable the renv cache to install packages directly into the R library +ENV RENV_CONFIG_CACHE_ENABLED=FALSE + +# Copy conda lock file to image +COPY conda-lock.yml conda-lock.yml + +# restore from conda-lock.yml file and clean up to reduce image size +RUN conda-lock install -n ${ENV_NAME} conda-lock.yml \ + && conda clean --all --yes + +# Copy the renv.lock file from the host environment to the image +COPY renv.lock renv.lock + +# restore from renv.lock file and clean up to reduce image size +RUN Rscript -e 'renv::restore()' \ + && rm -rf ~/.cache/R/renv \ + && rm -rf /tmp/downloaded_packages \ + && rm -rf /tmp/Rtmp* + +# Activate conda environment on bash launch +RUN echo "conda activate ${ENV_NAME}" >> ~/.bashrc + +# Set CMD to bash to activate the environment when launching +CMD ["/bin/bash"] diff --git a/analyses/cell-type-ETP-ALL-03/README.md b/analyses/cell-type-ETP-ALL-03/README.md new file mode 100644 index 000000000..d713df3ab --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/README.md @@ -0,0 +1,85 @@ +# ETP T-ALL Annotation (SCPCP000003) + +This analysis module will include codes to annotate cell types and tumor/normal status in ETP T-ALL from SCPCP000003 (n=30) present on the ScPCA portal. + +## Description + +We first aim to annotate the cell types in ETP T-ALL, and use the annotated B cells in the sample as the "normal" cells to identify tumor cells, since T-ALL is caused by the clonal proliferation of immature T-cell []. + +- We use the cell type marker (`Azimuth_BM_level1.csv`) from [Azimuth Human Bone Marrow reference](https://azimuth.hubmapconsortium.org/references/#Human%20-%20Bone%20Marrow). In total, there are 14 cell types: B, CD4T, CD8T, Other T, DC, Monocytes, Macrophages, NK, Early Erythrocytes, Late Erythrocytes, Plasma, Platelet, Stromal, and Hematopoietic Stem and Progenitor Cells (HSPC). Based on the exploratory analysis, we believe that most of the cells in these samples do not express adequate markers to be distinguished at finer cell type level (eg. naive vs memory, CD14 vs CD16 etc.), and majority of the cells should belong to T-cells. In addition, we include the marker genes for blast cell [[Bhasin et al. (2023)](https://www.nature.com/articles/s41598-023-39152-z)] as well as erythroid precursor and cancer cell in immune system [[ScType](https://sctype.app/database.php) database]. + +- Since ScType annotates cell types at cluster level using marker genes provided by user or from the built-in database, we employ [self-assembling manifold](https://github.com/atarashansky/self-assembling-manifold/tree/master) (SAM) algorithm, a soft feature selection strategy for better separation of homogeneous cell types. + +- After cell type annotation, we provide B cells as the normal cells in the sample, if there is any, to [CopyKat](https://github.com/navinlabcode/copykat), for identification of tumor cells. + +Here are the steps in the module: + +1. Generating a processed rds file for each sample using SAM (`scripts/00-01_processing_rds.R`) + +2. Annotating cell type using ScType and identifying tumor cells using CopyKat (`scripts/02-03_annotation.R`) + +## Usage + +Before running Rscripts in R or Rstudio, we first need to prepare the input files as shown in the next section, and run the following codes in the terminal for installing required libraries: + +``` +#system packages installation +sudo apt install libglpk40 +sudo apt install libcurl4-openssl-dev #for Seurat +sudo apt-get install libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libtiff5-dev #for devtools + +conda-lock install --name openscpca-cell-type-ETP-ALL-03 conda-lock.yml +Rscript -e "renv::restore()" +``` + +## Input files + +The `scripts/00-01_processing_rds.R` requires the processed SingleCellExperiment objects (`_processed.rds`) and doublet-detection results (`_processed_scdblfinder.tsv`) from SCPCP000003. These files could be obtained from running the following codes: + +``` +#run in terminal +../../download-data.py --projects SCPCP000003 +../../download-results.py --projects SCPCP000003 --modules doublet-detection +``` + +As for the annotation, `scripts/02-03_annotation.R` requires cell type marker gene file, `Azimuth_BM_level1.csv`, as an input for ScType. This excel file contains a list of positive marker genes in Ensembl ID under `ensembl_id_positive_marker` for each cell type; *TMEM56* and *CD235a* are not detected in our dataset, thus they are being removed as part of the markers for Late Eryth and Pre Eryth respectively. As of now, there is no negative marker genes provided under `ensembl_id_negative_marker`. + +## Output files + +Running `scripts/00-01_processing_rds.R` will generate two types of output: + +- `rds` objects in `scratch/` + +- umap plots showing leiden clustering in `plots/` + +Running `scripts/02-03_annotation.R` will generate several outputs: + +- updated `rds` objects in `scratch/` + +- umap plots showing cell type and CopyKat prediction (if there is any) and dotplots showing the features added with `AddModuleScore()` in `plots/` + +- ScType results of top 10 possible cell types in a cluster (`_sctype_top10_celltypes_perCluster.txt`) and metadata file tabulating leiden cluster, cell type, low confidence cell type, and CopyKat prediction for each cell (`_metadata.txt`) in `results/` + +## Software requirements + +To run the analysis, execute the Rscript in R or Rstudio (version 4.4.0). The main libraries used are: + +- Seurat (version 5.1.0) + +- reticulate (version 1.39.0) + +- sam-algorithm (in python) + +- ScType + +- CopyKat + +The renv.lock file contains all packages and version information. All python libraries are installed in the conda environment `openscpca-cell-type-ETP-ALL-03`, and the python codes are executed in the same environment by running them in R via `reticulate`. To create and activate this environment from `.yml` file use: + +``` +conda-lock install --name openscpca-cell-type-ETP-ALL-03 conda-lock.yml +``` + +## Computational resources + +All the commands above are currently executed in the standard 4XL virtual machine via AWS Lightsail for Research, but it runs pretty slow for CopyKat with one computational core. diff --git a/analyses/cell-type-ETP-ALL-03/cell-type-ETP-ALL-03.Rproj b/analyses/cell-type-ETP-ALL-03/cell-type-ETP-ALL-03.Rproj new file mode 100644 index 000000000..8e3c2ebc9 --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/cell-type-ETP-ALL-03.Rproj @@ -0,0 +1,13 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX diff --git a/analyses/cell-type-ETP-ALL-03/components/dependencies.R b/analyses/cell-type-ETP-ALL-03/components/dependencies.R new file mode 100644 index 000000000..ae80dc0ac --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/components/dependencies.R @@ -0,0 +1,2 @@ +# R dependencies not captured by `renv` +# library("missing_package") diff --git a/analyses/cell-type-ETP-ALL-03/conda-lock.yml b/analyses/cell-type-ETP-ALL-03/conda-lock.yml new file mode 100644 index 000000000..bc4edee0a --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/conda-lock.yml @@ -0,0 +1,7115 @@ +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV conda-lock.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile conda-lock.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f environment.yml --lockfile conda-lock.yml +version: 1 +metadata: + content_hash: + linux-64: ab1eae894f69694d0e06e29b31a804b77bf5bb88c385a1a6940219e4f54b89ca + osx-64: a589c43136f7c3a05cfc8461182215c737bda3bb5cf17c15248f6b768ead4286 + osx-arm64: 3fbc10608222233934eed4714c20aa520f9639aa3e93a3329809e5eef65bf83d + channels: + - url: conda-forge + used_env_vars: [] + - url: bioconda + used_env_vars: [] + platforms: + - linux-64 + - osx-64 + - 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/dev/null +++ b/analyses/cell-type-ETP-ALL-03/renv/.gitignore @@ -0,0 +1,7 @@ +library/ +local/ +cellar/ +lock/ +python/ +sandbox/ +staging/ diff --git a/analyses/cell-type-ETP-ALL-03/renv/activate.R b/analyses/cell-type-ETP-ALL-03/renv/activate.R new file mode 100644 index 000000000..d13f9932a --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/renv/activate.R @@ -0,0 +1,1220 @@ + +local({ + + # the requested version of renv + version <- "1.0.7" + attr(version, "sha") <- NULL + + # the project directory + project <- Sys.getenv("RENV_PROJECT") + if (!nzchar(project)) + project <- getwd() + + # use start-up diagnostics if enabled + diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE") + if (diagnostics) { + start <- Sys.time() + profile <- tempfile("renv-startup-", fileext = ".Rprof") + utils::Rprof(profile) + on.exit({ + utils::Rprof(NULL) + elapsed <- signif(difftime(Sys.time(), start, units = "auto"), digits = 2L) + writeLines(sprintf("- renv took %s to run the autoloader.", format(elapsed))) + writeLines(sprintf("- Profile: %s", profile)) + print(utils::summaryRprof(profile)) + }, add = TRUE) + } + + # figure out whether the autoloader is enabled + enabled <- local({ + + # first, check config option + override <- getOption("renv.config.autoloader.enabled") + if (!is.null(override)) + return(override) + + # if we're being run in a context where R_LIBS is already set, + # don't load -- presumably we're being run as a sub-process and + # the parent process has already set up library paths for us + rcmd <- Sys.getenv("R_CMD", unset = NA) + rlibs <- Sys.getenv("R_LIBS", unset = NA) + if (!is.na(rlibs) && !is.na(rcmd)) + return(FALSE) + + # next, check environment variables + # TODO: prefer using the configuration one in the future + envvars <- c( + "RENV_CONFIG_AUTOLOADER_ENABLED", + "RENV_AUTOLOADER_ENABLED", + "RENV_ACTIVATE_PROJECT" + ) + + for (envvar in envvars) { + envval <- Sys.getenv(envvar, unset = NA) + if (!is.na(envval)) + return(tolower(envval) %in% c("true", "t", "1")) + } + + # enable by default + TRUE + + }) + + # bail if we're not enabled + if (!enabled) { + + # if we're not enabled, we might still need to manually load + # the user profile here + profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile") + if (file.exists(profile)) { + cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE") + if (tolower(cfg) %in% c("true", "t", "1")) + sys.source(profile, envir = globalenv()) + } + + return(FALSE) + + } + + # avoid recursion + if (identical(getOption("renv.autoloader.running"), TRUE)) { + warning("ignoring recursive attempt to run renv autoloader") + return(invisible(TRUE)) + } + + # signal that we're loading renv during R startup + options(renv.autoloader.running = TRUE) + on.exit(options(renv.autoloader.running = NULL), add = TRUE) + + # signal that we've consented to use renv + options(renv.consent = TRUE) + + # load the 'utils' package eagerly -- this ensures that renv shims, which + # mask 'utils' packages, will come first on the search path + library(utils, lib.loc = .Library) + + # unload renv if it's already been loaded + if ("renv" %in% loadedNamespaces()) + unloadNamespace("renv") + + # load bootstrap tools + `%||%` <- function(x, y) { + if (is.null(x)) y else x + } + + catf <- function(fmt, ..., appendLF = TRUE) { + + quiet <- getOption("renv.bootstrap.quiet", default = FALSE) + if (quiet) + return(invisible()) + + msg <- sprintf(fmt, ...) + cat(msg, file = stdout(), sep = if (appendLF) "\n" else "") + + invisible(msg) + + } + + header <- function(label, + ..., + prefix = "#", + suffix = "-", + n = min(getOption("width"), 78)) + { + label <- sprintf(label, ...) + n <- max(n - nchar(label) - nchar(prefix) - 2L, 8L) + if (n <= 0) + return(paste(prefix, label)) + + tail <- paste(rep.int(suffix, n), collapse = "") + paste0(prefix, " ", label, " ", tail) + + } + + heredoc <- function(text, leave = 0) { + + # remove leading, trailing whitespace + trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text) + + # split into lines + lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]] + + # compute common indent + indent <- regexpr("[^[:space:]]", lines) + common <- min(setdiff(indent, -1L)) - leave + paste(substring(lines, common), collapse = "\n") + + } + + startswith <- function(string, prefix) { + substring(string, 1, nchar(prefix)) == prefix + } + + bootstrap <- function(version, library) { + + friendly <- renv_bootstrap_version_friendly(version) + section <- header(sprintf("Bootstrapping renv %s", friendly)) + catf(section) + + # attempt to download renv + catf("- Downloading renv ... ", appendLF = FALSE) + withCallingHandlers( + tarball <- renv_bootstrap_download(version), + error = function(err) { + catf("FAILED") + stop("failed to download:\n", conditionMessage(err)) + } + ) + catf("OK") + on.exit(unlink(tarball), add = TRUE) + + # now attempt to install + catf("- Installing renv ... ", appendLF = FALSE) + withCallingHandlers( + status <- renv_bootstrap_install(version, tarball, library), + error = function(err) { + catf("FAILED") + stop("failed to install:\n", conditionMessage(err)) + } + ) + catf("OK") + + # add empty line to break up bootstrapping from normal output + catf("") + + return(invisible()) + } + + renv_bootstrap_tests_running <- function() { + getOption("renv.tests.running", default = FALSE) + } + + renv_bootstrap_repos <- function() { + + # get CRAN repository + cran <- getOption("renv.repos.cran", "https://cloud.r-project.org") + + # check for repos override + repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA) + if (!is.na(repos)) { + + # check for RSPM; if set, use a fallback repository for renv + rspm <- Sys.getenv("RSPM", unset = NA) + if (identical(rspm, repos)) + repos <- c(RSPM = rspm, CRAN = cran) + + return(repos) + + } + + # check for lockfile repositories + repos <- tryCatch(renv_bootstrap_repos_lockfile(), error = identity) + if (!inherits(repos, "error") && length(repos)) + return(repos) + + # retrieve current repos + repos <- getOption("repos") + + # ensure @CRAN@ entries are resolved + repos[repos == "@CRAN@"] <- cran + + # add in renv.bootstrap.repos if set + default <- c(FALLBACK = "https://cloud.r-project.org") + extra <- getOption("renv.bootstrap.repos", default = default) + repos <- c(repos, extra) + + # remove duplicates that might've snuck in + dupes <- duplicated(repos) | duplicated(names(repos)) + repos[!dupes] + + } + + renv_bootstrap_repos_lockfile <- function() { + + lockpath <- Sys.getenv("RENV_PATHS_LOCKFILE", unset = "renv.lock") + if (!file.exists(lockpath)) + return(NULL) + + lockfile <- tryCatch(renv_json_read(lockpath), error = identity) + if (inherits(lockfile, "error")) { + warning(lockfile) + return(NULL) + } + + repos <- lockfile$R$Repositories + if (length(repos) == 0) + return(NULL) + + keys <- vapply(repos, `[[`, "Name", FUN.VALUE = character(1)) + vals <- vapply(repos, `[[`, "URL", FUN.VALUE = character(1)) + names(vals) <- keys + + return(vals) + + } + + renv_bootstrap_download <- function(version) { + + sha <- attr(version, "sha", exact = TRUE) + + methods <- if (!is.null(sha)) { + + # attempting to bootstrap a development version of renv + c( + function() renv_bootstrap_download_tarball(sha), + function() renv_bootstrap_download_github(sha) + ) + + } else { + + # attempting to bootstrap a release version of renv + c( + function() renv_bootstrap_download_tarball(version), + function() renv_bootstrap_download_cran_latest(version), + function() renv_bootstrap_download_cran_archive(version) + ) + + } + + for (method in methods) { + path <- tryCatch(method(), error = identity) + if (is.character(path) && file.exists(path)) + return(path) + } + + stop("All download methods failed") + + } + + renv_bootstrap_download_impl <- function(url, destfile) { + + mode <- "wb" + + # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715 + fixup <- + Sys.info()[["sysname"]] == "Windows" && + substring(url, 1L, 5L) == "file:" + + if (fixup) + mode <- "w+b" + + args <- list( + url = url, + destfile = destfile, + mode = mode, + quiet = TRUE + ) + + if ("headers" %in% names(formals(utils::download.file))) + args$headers <- renv_bootstrap_download_custom_headers(url) + + do.call(utils::download.file, args) + + } + + renv_bootstrap_download_custom_headers <- function(url) { + + headers <- getOption("renv.download.headers") + if (is.null(headers)) + return(character()) + + if (!is.function(headers)) + stopf("'renv.download.headers' is not a function") + + headers <- headers(url) + if (length(headers) == 0L) + return(character()) + + if (is.list(headers)) + headers <- unlist(headers, recursive = FALSE, use.names = TRUE) + + ok <- + is.character(headers) && + is.character(names(headers)) && + all(nzchar(names(headers))) + + if (!ok) + stop("invocation of 'renv.download.headers' did not return a named character vector") + + headers + + } + + renv_bootstrap_download_cran_latest <- function(version) { + + spec <- renv_bootstrap_download_cran_latest_find(version) + type <- spec$type + repos <- spec$repos + + baseurl <- utils::contrib.url(repos = repos, type = type) + ext <- if (identical(type, "source")) + ".tar.gz" + else if (Sys.info()[["sysname"]] == "Windows") + ".zip" + else + ".tgz" + name <- sprintf("renv_%s%s", version, ext) + url <- paste(baseurl, name, sep = "/") + + destfile <- file.path(tempdir(), name) + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (inherits(status, "condition")) + return(FALSE) + + # report success and return + destfile + + } + + renv_bootstrap_download_cran_latest_find <- function(version) { + + # check whether binaries are supported on this system + binary <- + getOption("renv.bootstrap.binary", default = TRUE) && + !identical(.Platform$pkgType, "source") && + !identical(getOption("pkgType"), "source") && + Sys.info()[["sysname"]] %in% c("Darwin", "Windows") + + types <- c(if (binary) "binary", "source") + + # iterate over types + repositories + for (type in types) { + for (repos in renv_bootstrap_repos()) { + + # retrieve package database + db <- tryCatch( + as.data.frame( + utils::available.packages(type = type, repos = repos), + stringsAsFactors = FALSE + ), + error = identity + ) + + if (inherits(db, "error")) + next + + # check for compatible entry + entry <- db[db$Package %in% "renv" & db$Version %in% version, ] + if (nrow(entry) == 0) + next + + # found it; return spec to caller + spec <- list(entry = entry, type = type, repos = repos) + return(spec) + + } + } + + # if we got here, we failed to find renv + fmt <- "renv %s is not available from your declared package repositories" + stop(sprintf(fmt, version)) + + } + + renv_bootstrap_download_cran_archive <- function(version) { + + name <- sprintf("renv_%s.tar.gz", version) + repos <- renv_bootstrap_repos() + urls <- file.path(repos, "src/contrib/Archive/renv", name) + destfile <- file.path(tempdir(), name) + + for (url in urls) { + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (identical(status, 0L)) + return(destfile) + + } + + return(FALSE) + + } + + renv_bootstrap_download_tarball <- function(version) { + + # if the user has provided the path to a tarball via + # an environment variable, then use it + tarball <- Sys.getenv("RENV_BOOTSTRAP_TARBALL", unset = NA) + if (is.na(tarball)) + return() + + # allow directories + if (dir.exists(tarball)) { + name <- sprintf("renv_%s.tar.gz", version) + tarball <- file.path(tarball, name) + } + + # bail if it doesn't exist + if (!file.exists(tarball)) { + + # let the user know we weren't able to honour their request + fmt <- "- RENV_BOOTSTRAP_TARBALL is set (%s) but does not exist." + msg <- sprintf(fmt, tarball) + warning(msg) + + # bail + return() + + } + + catf("- Using local tarball '%s'.", tarball) + tarball + + } + + renv_bootstrap_download_github <- function(version) { + + enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") + if (!identical(enabled, "TRUE")) + return(FALSE) + + # prepare download options + pat <- Sys.getenv("GITHUB_PAT") + if (nzchar(Sys.which("curl")) && nzchar(pat)) { + fmt <- "--location --fail --header \"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "curl", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } else if (nzchar(Sys.which("wget")) && nzchar(pat)) { + fmt <- "--header=\"Authorization: token %s\"" + extra <- sprintf(fmt, pat) + saved <- options("download.file.method", "download.file.extra") + options(download.file.method = "wget", download.file.extra = extra) + on.exit(do.call(base::options, saved), add = TRUE) + } + + url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version) + name <- sprintf("renv_%s.tar.gz", version) + destfile <- file.path(tempdir(), name) + + status <- tryCatch( + renv_bootstrap_download_impl(url, destfile), + condition = identity + ) + + if (!identical(status, 0L)) + return(FALSE) + + renv_bootstrap_download_augment(destfile) + + return(destfile) + + } + + # Add Sha to DESCRIPTION. This is stop gap until #890, after which we + # can use renv::install() to fully capture metadata. + renv_bootstrap_download_augment <- function(destfile) { + sha <- renv_bootstrap_git_extract_sha1_tar(destfile) + if (is.null(sha)) { + return() + } + + # Untar + tempdir <- tempfile("renv-github-") + on.exit(unlink(tempdir, recursive = TRUE), add = TRUE) + untar(destfile, exdir = tempdir) + pkgdir <- dir(tempdir, full.names = TRUE)[[1]] + + # Modify description + desc_path <- file.path(pkgdir, "DESCRIPTION") + desc_lines <- readLines(desc_path) + remotes_fields <- c( + "RemoteType: github", + "RemoteHost: api.github.com", + "RemoteRepo: renv", + "RemoteUsername: rstudio", + "RemotePkgRef: rstudio/renv", + paste("RemoteRef: ", sha), + paste("RemoteSha: ", sha) + ) + writeLines(c(desc_lines[desc_lines != ""], remotes_fields), con = desc_path) + + # Re-tar + local({ + old <- setwd(tempdir) + on.exit(setwd(old), add = TRUE) + + tar(destfile, compression = "gzip") + }) + invisible() + } + + # Extract the commit hash from a git archive. Git archives include the SHA1 + # hash as the comment field of the tarball pax extended header + # (see https://www.kernel.org/pub/software/scm/git/docs/git-archive.html) + # For GitHub archives this should be the first header after the default one + # (512 byte) header. + renv_bootstrap_git_extract_sha1_tar <- function(bundle) { + + # open the bundle for reading + # We use gzcon for everything because (from ?gzcon) + # > Reading from a connection which does not supply a 'gzip' magic + # > header is equivalent to reading from the original connection + conn <- gzcon(file(bundle, open = "rb", raw = TRUE)) + on.exit(close(conn)) + + # The default pax header is 512 bytes long and the first pax extended header + # with the comment should be 51 bytes long + # `52 comment=` (11 chars) + 40 byte SHA1 hash + len <- 0x200 + 0x33 + res <- rawToChar(readBin(conn, "raw", n = len)[0x201:len]) + + if (grepl("^52 comment=", res)) { + sub("52 comment=", "", res) + } else { + NULL + } + } + + renv_bootstrap_install <- function(version, tarball, library) { + + # attempt to install it into project library + dir.create(library, showWarnings = FALSE, recursive = TRUE) + output <- renv_bootstrap_install_impl(library, tarball) + + # check for successful install + status <- attr(output, "status") + if (is.null(status) || identical(status, 0L)) + return(status) + + # an error occurred; report it + header <- "installation of renv failed" + lines <- paste(rep.int("=", nchar(header)), collapse = "") + text <- paste(c(header, lines, output), collapse = "\n") + stop(text) + + } + + renv_bootstrap_install_impl <- function(library, tarball) { + + # invoke using system2 so we can capture and report output + bin <- R.home("bin") + exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R" + R <- file.path(bin, exe) + + args <- c( + "--vanilla", "CMD", "INSTALL", "--no-multiarch", + "-l", shQuote(path.expand(library)), + shQuote(path.expand(tarball)) + ) + + system2(R, args, stdout = TRUE, stderr = TRUE) + + } + + renv_bootstrap_platform_prefix <- function() { + + # construct version prefix + version <- paste(R.version$major, R.version$minor, sep = ".") + prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-") + + # include SVN revision for development versions of R + # (to avoid sharing platform-specific artefacts with released versions of R) + devel <- + identical(R.version[["status"]], "Under development (unstable)") || + identical(R.version[["nickname"]], "Unsuffered Consequences") + + if (devel) + prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r") + + # build list of path components + components <- c(prefix, R.version$platform) + + # include prefix if provided by user + prefix <- renv_bootstrap_platform_prefix_impl() + if (!is.na(prefix) && nzchar(prefix)) + components <- c(prefix, components) + + # build prefix + paste(components, collapse = "/") + + } + + renv_bootstrap_platform_prefix_impl <- function() { + + # if an explicit prefix has been supplied, use it + prefix <- Sys.getenv("RENV_PATHS_PREFIX", unset = NA) + if (!is.na(prefix)) + return(prefix) + + # if the user has requested an automatic prefix, generate it + auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) + if (is.na(auto) && getRversion() >= "4.4.0") + auto <- "TRUE" + + if (auto %in% c("TRUE", "True", "true", "1")) + return(renv_bootstrap_platform_prefix_auto()) + + # empty string on failure + "" + + } + + renv_bootstrap_platform_prefix_auto <- function() { + + prefix <- tryCatch(renv_bootstrap_platform_os(), error = identity) + if (inherits(prefix, "error") || prefix %in% "unknown") { + + msg <- paste( + "failed to infer current operating system", + "please file a bug report at https://github.com/rstudio/renv/issues", + sep = "; " + ) + + warning(msg) + + } + + prefix + + } + + renv_bootstrap_platform_os <- function() { + + sysinfo <- Sys.info() + sysname <- sysinfo[["sysname"]] + + # handle Windows + macOS up front + if (sysname == "Windows") + return("windows") + else if (sysname == "Darwin") + return("macos") + + # check for os-release files + for (file in c("/etc/os-release", "/usr/lib/os-release")) + if (file.exists(file)) + return(renv_bootstrap_platform_os_via_os_release(file, sysinfo)) + + # check for redhat-release files + if (file.exists("/etc/redhat-release")) + return(renv_bootstrap_platform_os_via_redhat_release()) + + "unknown" + + } + + renv_bootstrap_platform_os_via_os_release <- function(file, sysinfo) { + + # read /etc/os-release + release <- utils::read.table( + file = file, + sep = "=", + quote = c("\"", "'"), + col.names = c("Key", "Value"), + comment.char = "#", + stringsAsFactors = FALSE + ) + + vars <- as.list(release$Value) + names(vars) <- release$Key + + # get os name + os <- tolower(sysinfo[["sysname"]]) + + # read id + id <- "unknown" + for (field in c("ID", "ID_LIKE")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + id <- vars[[field]] + break + } + } + + # read version + version <- "unknown" + for (field in c("UBUNTU_CODENAME", "VERSION_CODENAME", "VERSION_ID", "BUILD_ID")) { + if (field %in% names(vars) && nzchar(vars[[field]])) { + version <- vars[[field]] + break + } + } + + # join together + paste(c(os, id, version), collapse = "-") + + } + + renv_bootstrap_platform_os_via_redhat_release <- function() { + + # read /etc/redhat-release + contents <- readLines("/etc/redhat-release", warn = FALSE) + + # infer id + id <- if (grepl("centos", contents, ignore.case = TRUE)) + "centos" + else if (grepl("redhat", contents, ignore.case = TRUE)) + "redhat" + else + "unknown" + + # try to find a version component (very hacky) + version <- "unknown" + + parts <- strsplit(contents, "[[:space:]]")[[1L]] + for (part in parts) { + + nv <- tryCatch(numeric_version(part), error = identity) + if (inherits(nv, "error")) + next + + version <- nv[1, 1] + break + + } + + paste(c("linux", id, version), collapse = "-") + + } + + renv_bootstrap_library_root_name <- function(project) { + + # use project name as-is if requested + asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE") + if (asis) + return(basename(project)) + + # otherwise, disambiguate based on project's path + id <- substring(renv_bootstrap_hash_text(project), 1L, 8L) + paste(basename(project), id, sep = "-") + + } + + renv_bootstrap_library_root <- function(project) { + + prefix <- renv_bootstrap_profile_prefix() + + path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA) + if (!is.na(path)) + return(paste(c(path, prefix), collapse = "/")) + + path <- renv_bootstrap_library_root_impl(project) + if (!is.null(path)) { + name <- renv_bootstrap_library_root_name(project) + return(paste(c(path, prefix, name), collapse = "/")) + } + + renv_bootstrap_paths_renv("library", project = project) + + } + + renv_bootstrap_library_root_impl <- function(project) { + + root <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA) + if (!is.na(root)) + return(root) + + type <- renv_bootstrap_project_type(project) + if (identical(type, "package")) { + userdir <- renv_bootstrap_user_dir() + return(file.path(userdir, "library")) + } + + } + + renv_bootstrap_validate_version <- function(version, description = NULL) { + + # resolve description file + # + # avoid passing lib.loc to `packageDescription()` below, since R will + # use the loaded version of the package by default anyhow. note that + # this function should only be called after 'renv' is loaded + # https://github.com/rstudio/renv/issues/1625 + description <- description %||% packageDescription("renv") + + # check whether requested version 'version' matches loaded version of renv + sha <- attr(version, "sha", exact = TRUE) + valid <- if (!is.null(sha)) + renv_bootstrap_validate_version_dev(sha, description) + else + renv_bootstrap_validate_version_release(version, description) + + if (valid) + return(TRUE) + + # the loaded version of renv doesn't match the requested version; + # give the user instructions on how to proceed + dev <- identical(description[["RemoteType"]], "github") + remote <- if (dev) + paste("rstudio/renv", description[["RemoteSha"]], sep = "@") + else + paste("renv", description[["Version"]], sep = "@") + + # display both loaded version + sha if available + friendly <- renv_bootstrap_version_friendly( + version = description[["Version"]], + sha = if (dev) description[["RemoteSha"]] + ) + + fmt <- heredoc(" + renv %1$s was loaded from project library, but this project is configured to use renv %2$s. + - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile. + - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library. + ") + catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) + + FALSE + + } + + renv_bootstrap_validate_version_dev <- function(version, description) { + expected <- description[["RemoteSha"]] + is.character(expected) && startswith(expected, version) + } + + renv_bootstrap_validate_version_release <- function(version, description) { + expected <- description[["Version"]] + is.character(expected) && identical(expected, version) + } + + renv_bootstrap_hash_text <- function(text) { + + hashfile <- tempfile("renv-hash-") + on.exit(unlink(hashfile), add = TRUE) + + writeLines(text, con = hashfile) + tools::md5sum(hashfile) + + } + + renv_bootstrap_load <- function(project, libpath, version) { + + # try to load renv from the project library + if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) + return(FALSE) + + # warn if the version of renv loaded does not match + renv_bootstrap_validate_version(version) + + # execute renv load hooks, if any + hooks <- getHook("renv::autoload") + for (hook in hooks) + if (is.function(hook)) + tryCatch(hook(), error = warnify) + + # load the project + renv::load(project) + + TRUE + + } + + renv_bootstrap_profile_load <- function(project) { + + # if RENV_PROFILE is already set, just use that + profile <- Sys.getenv("RENV_PROFILE", unset = NA) + if (!is.na(profile) && nzchar(profile)) + return(profile) + + # check for a profile file (nothing to do if it doesn't exist) + path <- renv_bootstrap_paths_renv("profile", profile = FALSE, project = project) + if (!file.exists(path)) + return(NULL) + + # read the profile, and set it if it exists + contents <- readLines(path, warn = FALSE) + if (length(contents) == 0L) + return(NULL) + + # set RENV_PROFILE + profile <- contents[[1L]] + if (!profile %in% c("", "default")) + Sys.setenv(RENV_PROFILE = profile) + + profile + + } + + renv_bootstrap_profile_prefix <- function() { + profile <- renv_bootstrap_profile_get() + if (!is.null(profile)) + return(file.path("profiles", profile, "renv")) + } + + renv_bootstrap_profile_get <- function() { + profile <- Sys.getenv("RENV_PROFILE", unset = "") + renv_bootstrap_profile_normalize(profile) + } + + renv_bootstrap_profile_set <- function(profile) { + profile <- renv_bootstrap_profile_normalize(profile) + if (is.null(profile)) + Sys.unsetenv("RENV_PROFILE") + else + Sys.setenv(RENV_PROFILE = profile) + } + + renv_bootstrap_profile_normalize <- function(profile) { + + if (is.null(profile) || profile %in% c("", "default")) + return(NULL) + + profile + + } + + renv_bootstrap_path_absolute <- function(path) { + + substr(path, 1L, 1L) %in% c("~", "/", "\\") || ( + substr(path, 1L, 1L) %in% c(letters, LETTERS) && + substr(path, 2L, 3L) %in% c(":/", ":\\") + ) + + } + + renv_bootstrap_paths_renv <- function(..., profile = TRUE, project = NULL) { + renv <- Sys.getenv("RENV_PATHS_RENV", unset = "renv") + root <- if (renv_bootstrap_path_absolute(renv)) NULL else project + prefix <- if (profile) renv_bootstrap_profile_prefix() + components <- c(root, renv, prefix, ...) + paste(components, collapse = "/") + } + + renv_bootstrap_project_type <- function(path) { + + descpath <- file.path(path, "DESCRIPTION") + if (!file.exists(descpath)) + return("unknown") + + desc <- tryCatch( + read.dcf(descpath, all = TRUE), + error = identity + ) + + if (inherits(desc, "error")) + return("unknown") + + type <- desc$Type + if (!is.null(type)) + return(tolower(type)) + + package <- desc$Package + if (!is.null(package)) + return("package") + + "unknown" + + } + + renv_bootstrap_user_dir <- function() { + dir <- renv_bootstrap_user_dir_impl() + path.expand(chartr("\\", "/", dir)) + } + + renv_bootstrap_user_dir_impl <- function() { + + # use local override if set + override <- getOption("renv.userdir.override") + if (!is.null(override)) + return(override) + + # use R_user_dir if available + tools <- asNamespace("tools") + if (is.function(tools$R_user_dir)) + return(tools$R_user_dir("renv", "cache")) + + # try using our own backfill for older versions of R + envvars <- c("R_USER_CACHE_DIR", "XDG_CACHE_HOME") + for (envvar in envvars) { + root <- Sys.getenv(envvar, unset = NA) + if (!is.na(root)) + return(file.path(root, "R/renv")) + } + + # use platform-specific default fallbacks + if (Sys.info()[["sysname"]] == "Windows") + file.path(Sys.getenv("LOCALAPPDATA"), "R/cache/R/renv") + else if (Sys.info()[["sysname"]] == "Darwin") + "~/Library/Caches/org.R-project.R/R/renv" + else + "~/.cache/R/renv" + + } + + renv_bootstrap_version_friendly <- function(version, shafmt = NULL, sha = NULL) { + sha <- sha %||% attr(version, "sha", exact = TRUE) + parts <- c(version, sprintf(shafmt %||% " [sha: %s]", substring(sha, 1L, 7L))) + paste(parts, collapse = "") + } + + renv_bootstrap_exec <- function(project, libpath, version) { + if (!renv_bootstrap_load(project, libpath, version)) + renv_bootstrap_run(version, libpath) + } + + renv_bootstrap_run <- function(version, libpath) { + + # perform bootstrap + bootstrap(version, libpath) + + # exit early if we're just testing bootstrap + if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA))) + return(TRUE) + + # try again to load + if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) { + return(renv::load(project = getwd())) + } + + # failed to download or load renv; warn the user + msg <- c( + "Failed to find an renv installation: the project will not be loaded.", + "Use `renv::activate()` to re-initialize the project." + ) + + warning(paste(msg, collapse = "\n"), call. = FALSE) + + } + + renv_json_read <- function(file = NULL, text = NULL) { + + jlerr <- NULL + + # if jsonlite is loaded, use that instead + if ("jsonlite" %in% loadedNamespaces()) { + + json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + jlerr <- json + + } + + # otherwise, fall back to the default JSON reader + json <- tryCatch(renv_json_read_default(file, text), error = identity) + if (!inherits(json, "error")) + return(json) + + # report an error + if (!is.null(jlerr)) + stop(jlerr) + else + stop(json) + + } + + renv_json_read_jsonlite <- function(file = NULL, text = NULL) { + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + jsonlite::fromJSON(txt = text, simplifyVector = FALSE) + } + + renv_json_read_default <- function(file = NULL, text = NULL) { + + # find strings in the JSON + text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n") + pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' + locs <- gregexpr(pattern, text, perl = TRUE)[[1]] + + # if any are found, replace them with placeholders + replaced <- text + strings <- character() + replacements <- character() + + if (!identical(c(locs), -1L)) { + + # get the string values + starts <- locs + ends <- locs + attr(locs, "match.length") - 1L + strings <- substring(text, starts, ends) + + # only keep those requiring escaping + strings <- grep("[[\\]{}:]", strings, perl = TRUE, value = TRUE) + + # compute replacements + replacements <- sprintf('"\032%i\032"', seq_along(strings)) + + # replace the strings + mapply(function(string, replacement) { + replaced <<- sub(string, replacement, replaced, fixed = TRUE) + }, strings, replacements) + + } + + # transform the JSON into something the R parser understands + transformed <- replaced + transformed <- gsub("{}", "`names<-`(list(), character())", transformed, fixed = TRUE) + transformed <- gsub("[[{]", "list(", transformed, perl = TRUE) + transformed <- gsub("[]}]", ")", transformed, perl = TRUE) + transformed <- gsub(":", "=", transformed, fixed = TRUE) + text <- paste(transformed, collapse = "\n") + + # parse it + json <- parse(text = text, keep.source = FALSE, srcfile = NULL)[[1L]] + + # construct map between source strings, replaced strings + map <- as.character(parse(text = strings)) + names(map) <- as.character(parse(text = replacements)) + + # convert to list + map <- as.list(map) + + # remap strings in object + remapped <- renv_json_read_remap(json, map) + + # evaluate + eval(remapped, envir = baseenv()) + + } + + renv_json_read_remap <- function(json, map) { + + # fix names + if (!is.null(names(json))) { + lhs <- match(names(json), names(map), nomatch = 0L) + rhs <- match(names(map), names(json), nomatch = 0L) + names(json)[rhs] <- map[lhs] + } + + # fix values + if (is.character(json)) + return(map[[json]] %||% json) + + # handle true, false, null + if (is.name(json)) { + text <- as.character(json) + if (text == "true") + return(TRUE) + else if (text == "false") + return(FALSE) + else if (text == "null") + return(NULL) + } + + # recurse + if (is.recursive(json)) { + for (i in seq_along(json)) { + json[i] <- list(renv_json_read_remap(json[[i]], map)) + } + } + + json + + } + + # load the renv profile, if any + renv_bootstrap_profile_load(project) + + # construct path to library root + root <- renv_bootstrap_library_root(project) + + # construct library prefix for platform + prefix <- renv_bootstrap_platform_prefix() + + # construct full libpath + libpath <- file.path(root, prefix) + + # run bootstrap code + renv_bootstrap_exec(project, libpath, version) + + invisible() + +}) diff --git a/analyses/cell-type-ETP-ALL-03/renv/settings.json b/analyses/cell-type-ETP-ALL-03/renv/settings.json new file mode 100644 index 000000000..96e0d180f --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/renv/settings.json @@ -0,0 +1,5 @@ +{ + "bioconductor.version": "3.19", + "ppm.enabled": true, + "r.version": "4.4.0" +} diff --git a/analyses/cell-type-ETP-ALL-03/results/README.md b/analyses/cell-type-ETP-ALL-03/results/README.md new file mode 100644 index 000000000..fdb40dd83 --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/results/README.md @@ -0,0 +1,16 @@ +# Results directory instructions + +Run the following codes to sync the results in a Lightsail virtual computer: + +``` +cd /home/lightsail-user/OpenScPCA-analysis +scripts/sync-results.py cell-type-ETP-ALL-03 --bucket researcher-650251722463-us-east-2 +``` + +These are the generated outputs for each sample in the S3 bucket: + +- `rds` objects: `s3://researcher-650251722463-us-east-2/cell-type-ETP-ALL-03/results/rds` + +- metadata and ScType results: `s3://researcher-650251722463-us-east-2/cell-type-ETP-ALL-03/results/` + +- umap and dot plots: `s3://researcher-650251722463-us-east-2/cell-type-ETP-ALL-03/plots` diff --git a/analyses/cell-type-ETP-ALL-03/scratch/.gitkeep b/analyses/cell-type-ETP-ALL-03/scratch/.gitkeep new file mode 100644 index 000000000..e69de29bb diff --git a/analyses/cell-type-ETP-ALL-03/scripts/.gitkeep b/analyses/cell-type-ETP-ALL-03/scripts/.gitkeep new file mode 100644 index 000000000..e69de29bb diff --git a/analyses/cell-type-ETP-ALL-03/scripts/00-01_processing_rds.R b/analyses/cell-type-ETP-ALL-03/scripts/00-01_processing_rds.R new file mode 100644 index 000000000..ef3ccf42e --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/scripts/00-01_processing_rds.R @@ -0,0 +1,62 @@ +#!/usr/bin/env Rscript + +#This script uses SAM algorithm to perform soft feature selection for better separation of homogenous populations. +#So we use SAM to preprocess the data, perform feature selection/dimensionality reduction and clustering. +#The outputs are an intermediate rds file and umap plot showing leiden clustering results. + +library(Seurat) +library(SingleCellExperiment) +library(ggplot2) +######## step01 ####################################### +library(reticulate) +use_condaenv("openscpca-cell-type-ETP-ALL-03") +samalg <- import("samalg") #https://github.com/atarashansky/self-assembling-manifold/tree/master + +run_sam <- function(ind.sample, ind.library){ + sce <- readRDS(file.path(data_loc,ind.sample,paste0(ind.library,"_processed.rds"))) + + #reading in doublets information + doublets.data <- read.table(file = file.path(doublet_loc,ind.sample,paste0(ind.library,"_processed_scdblfinder.tsv")), + sep = "\t", header = T) + idx <- match(colnames(sce), doublets.data$barcodes) + sce$doublet_class <- doublets.data$class[idx] + sce <- sce[, which(sce$subsets_mito_percent < 25)] + + #step 01 feature selection/dimensionality using SAM + sam = samalg$SAM(counts = c(r_to_py(t(counts(sce))), + r_to_py(as.array(rownames(sce))), + r_to_py(as.array(colnames(sce))))) + sam$preprocess_data() + sam$run(distance = 'correlation') + sam$clustering(method = "leiden") #leiden clustering is the default algorithm in SAM + sam$save_anndata(paste0("sam.",ind.library,".h5ad")) + + final.obj <- schard::h5ad2seurat(paste0("sam.",ind.library,".h5ad")) + final.obj <- AddMetaData(final.obj, as.data.frame(colData(sce))) + final.obj[["RNA"]]@counts <- counts(sce) + final.obj[["RNA"]] <- AddMetaData(final.obj[["RNA"]], as.data.frame(rowData(sce))) + final.obj$nCount_RNA <- final.obj$sum + final.obj$nFeature_RNA <- final.obj$detected + # create a new assay to store ADT information + final.obj[["ADT"]] <- CreateAssayObject(counts = counts(altExp(sce, "adt"))) + final.obj[["ADT"]]@data <- logcounts(altExp(sce, "adt")) + final.obj[["ADT"]] <- AddMetaData(final.obj[["ADT"]], as.data.frame(rowData(altExp(sce, "adt")))) + + saveRDS(final.obj, file.path(out_loc,"results/rds",paste0(ind.library,".rds"))) + unlink(paste0("sam.",ind.library,".h5ad")) +} + +project_root <- rprojroot::find_root(rprojroot::is_git_root) +projectID <- "SCPCP000003" +out_loc <- file.path(project_root, "analyses/cell-type-ETP-ALL-03") +data_loc <- file.path(project_root, "data/current",projectID) +doublet_loc <- file.path(project_root, "data/current/results/doublet-detection",projectID) +dir.create(file.path(out_loc, "results/rds"), showWarnings = FALSE) + +metadata <- read.table(file.path(data_loc,"single_cell_metadata.tsv"), sep = "\t", header = T) +metadata <- metadata[which(metadata$scpca_project_id == projectID & + metadata$diagnosis == "Early T-cell precursor T-cell acute lymphoblastic leukemia"), ] +sampleID <- metadata$scpca_sample_id +libraryID <- metadata$scpca_library_id + +purrr::walk2(sampleID, libraryID, run_sam) diff --git a/analyses/cell-type-ETP-ALL-03/scripts/02-03_annotation.R b/analyses/cell-type-ETP-ALL-03/scripts/02-03_annotation.R new file mode 100644 index 000000000..5b007aa0d --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/scripts/02-03_annotation.R @@ -0,0 +1,169 @@ +#!/usr/bin/env Rscript + +#This script uses ScType to perform cell type annotation and CopyKat for tumor cells identification. +#We provides Azimuth_BM_level1.csv as the marker files for ScType, and generates sctype_classification metadata for the seurat object +#We also provides the top 10 celltypes with the highest sctype score for each cluster in the results/. +#Based on the annotated B cells, we provide them as the normal cells for CopyKat to identify tumor cells. +#The outputs are final rds file and two umap plots showing cell type and tumor/normal cells status. + +library(dplyr) +library(Seurat) +library(HGNChelper) +library(copykat) +library(ggplot2) + +# load gene set preparation function +#source("https://raw.githubusercontent.com/IanevskiAleksandr/sc-type/master/R/gene_sets_prepare.R") +# load cell type annotation function +source("https://github.com/IanevskiAleksandr/sc-type/raw/6db9eef49f185cf4d79bfec92a20fcf1edcccafb/R/sctype_score_.R") + +gene_sets_prepare <- function(path_to_db_file, cell_type){ + cell_markers = read.csv(path_to_db_file, header = T) + cell_markers = cell_markers[cell_markers$tissueType == cell_type,] + cell_markers$ensembl_id_positive_marker = gsub(" ","",cell_markers$ensembl_id_positive_marker); cell_markers$ensembl_id_negative_marker = gsub(" ","",cell_markers$ensembl_id_negative_marker) + + # correct gene symbols from the given DB (up-genes) + cell_markers$ensembl_id_positive_marker = sapply(1:nrow(cell_markers), function(i){ + markers_all = gsub(" ", "", unlist(strsplit(cell_markers$ensembl_id_positive_marker[i],","))) + markers_all = toupper(markers_all[markers_all != "NA" & markers_all != ""]) + markers_all = sort(markers_all) + + if(length(markers_all) > 0){ + suppressMessages({markers_all = unique(na.omit(markers_all))}) #since the markers are provided in Ensembl ID, I removed checkGeneSymbols function here + paste0(markers_all, collapse=",") + } else { + "" + } + }) + + # correct gene symbols from the given DB (down-genes) + cell_markers$ensembl_id_negative_marker = sapply(1:nrow(cell_markers), function(i){ + markers_all = gsub(" ", "", unlist(strsplit(cell_markers$ensembl_id_negative_marker[i],","))) + markers_all = toupper(markers_all[markers_all != "NA" & markers_all != ""]) + markers_all = sort(markers_all) + + if(length(markers_all) > 0){ + suppressMessages({markers_all = unique(na.omit(markers_all))}) #since the markers are provided in Ensembl ID, I removed checkGeneSymbols function here + paste0(markers_all, collapse=",") + } else { + "" + } + }) + + cell_markers$ensembl_id_positive_marker = gsub("///",",",cell_markers$ensembl_id_positive_marker);cell_markers$ensembl_id_positive_marker = gsub(" ","",cell_markers$ensembl_id_positive_marker) + cell_markers$ensembl_id_negative_marker = gsub("///",",",cell_markers$ensembl_id_negative_marker);cell_markers$ensembl_id_negative_marker = gsub(" ","",cell_markers$ensembl_id_negative_marker) + + gs = lapply(1:nrow(cell_markers), function(j) gsub(" ","",unlist(strsplit(toString(cell_markers$ensembl_id_positive_marker[j]),",")))); names(gs) = cell_markers$cellName + gs2 = lapply(1:nrow(cell_markers), function(j) gsub(" ","",unlist(strsplit(toString(cell_markers$ensembl_id_negative_marker[j]),",")))); names(gs2) = cell_markers$cellName + + list(gs_positive = gs, gs_negative = gs2) +} + +running_scType <- function(gs_list, annot.obj, assay = "RNA", thres = 4){ + # check Seurat object version (scRNA-seq matrix extracted differently in Seurat v4/v5) + seurat_package_v5 <- isFALSE('counts' %in% names(attributes(annot.obj[[assay]]))); + print(sprintf("Seurat object %s is used", ifelse(seurat_package_v5, "v5", "v4"))) + # extract scaled scRNA-seq matrix + scRNAseqData_scaled <- if (seurat_package_v5) as.matrix(annot.obj[[assay]]$scale.data) else as.matrix(annot.obj[[assay]]@scale.data) + # run ScType (es.max is a table with #cell types as row and #cells as column, recording the sctype score for each cell/celltype combination) + es.max <- sctype_score(scRNAseqData = scRNAseqData_scaled, scaled = TRUE, gs = gs_list$gs_positive, gs2 = gs_list$gs_negative) + # merge by cluster [repetitively finding top 10 cell types with the highest total ScType score for each cluster] + ## es.max.cl - stores the descending value of total ScType score for each cell type in a particular cluster + ## The following line prints out the top 10 cell types with the highest total ScType score for a cluster, along with #cells in that cluster + ## which is then stored in cL_results (_sctype_top10_celltypes_perCluster.txt) - table with 4 columns (clusterID, cell type, total ScType score, #cells) + cL_results <- do.call("rbind", lapply(unique(annot.obj@meta.data$leiden_clusters), function(cl){ + es.max.cl = sort(rowSums(es.max[ ,rownames(annot.obj@meta.data[annot.obj@meta.data$leiden_clusters==cl, ])]), decreasing = !0) + head(data.frame(cluster = cl, type = names(es.max.cl), scores = es.max.cl, ncells = sum(annot.obj@meta.data$leiden_clusters==cl)), 10) + })) + sctype_scores <- cL_results %>% group_by(cluster) %>% top_n(n = 1, wt = scores) + # set low-confident (low ScType score) clusters to "unknown" + sctype_scores$type[as.numeric(as.character(sctype_scores$scores)) < sctype_scores$ncells/thres] <- "Unknown" + print(sctype_scores[,1:3]) + + annot.obj@meta.data$sctype_classification = "" + for(cluster_num in unique(sctype_scores$cluster)){ + cl_type = sctype_scores[sctype_scores$cluster==cluster_num,]; + annot.obj@meta.data$sctype_classification[annot.obj@meta.data$leiden_clusters == cluster_num] = as.character(cl_type$type[1]) + } + return (list(annot.obj, cL_results)) +} + +plot_modulescore <- function(gs_list, seu, sample.name){ + for (i in 1:length(gs_list$gs_positive)){ + seu <- AddModuleScore(object = seu, name = paste0(gsub(" ","",names(gs_list$gs_positive[i])),"_Features"), + features = list(gs_list$gs_positive[[i]])) + } + features.vec <- paste0(gsub(" ","",names(gs_list$gs_positive)),"_Features1") + Idents(seu) <- seu$leiden_clusters + DotPlot(seu, features = features.vec) + theme(axis.text.x = element_text(angle=45,hjust=1)) + + ggtitle(paste0(sample.name,": cell type module score")) + + scale_color_gradient2(low = scales::muted("blue"), mid = "whitesmoke", high = scales::muted("red"), midpoint = 0) + ggsave(file.path(out_loc,"plots",paste0(sample.name,"_features_dotplot.png")), width = 7, height = 7, bg = "white", dpi = 150) + return (seu) +} + +run_annot <- function(ind.lib){ + seu <- readRDS(file.path(out_loc,"results/rds",paste0(ind.lib,".rds"))) + final.obj <- seu #so I can keep an object without scale.data (it is taking too much space to save scale.data) + seu <- ScaleData(seu, features = rownames(seu)) + gs_list <- gene_sets_prepare(db, tissue) #prepare gene sets + ## relaxing the threshold of sctype_score larger than %ncells in a cluster, from 25% (default) to 10% + res <- running_scType(gs_list, seu, thres = 10) #cell type annotation + seu$lowConfidence_annot <- res[[1]]$sctype_classification #seurat object with 'sctype_classification' metadata added + res <- running_scType(gs_list, seu) + seu <- res[[1]] + #res[[2]] - A table with top 10 cell types with the highest scores for each cluster + write.table(res[[2]], file = file.path(out_loc,"results",paste0(ind.lib,"_sctype_top10_celltypes_perCluster.txt")), + row.names = F, sep = "\t", quote = F) + + seu <- plot_modulescore(gs_list, seu, ind.lib) + + #using copykat for tumor cells identification + special.lib <- c("SCPCL000055","SCPCL000066","SCPCL000709","SCPCL000696") + special.norm <- c(15,11,13,18) ## from manual checking of B cells location (should be separated if possible) + if (ind.lib %in% special.lib){ + norm.cells <- colnames(seu)[which(seu$leiden_clusters == special.norm[match(ind.lib,special.lib)])] + }else{ + norm.cells <- colnames(seu)[which(seu$sctype_classification=="B")] + } + + n_cores <- parallel::detectCores() - 1 + if (length(norm.cells) > 0){ #the sample has B cells annotated + copykat.test <- copykat(rawmat=seu@assays[["RNA"]]@counts, id.type="Ensemble", + ngene.chr=5, win.size=25, KS.cut=0.1, sam.name=ind.lib, + distance="euclidean", norm.cell.names=norm.cells, + output.seg="FALSE", plot.genes="TRUE", genome="hg20",n.cores=n_cores) + idx <- match(colnames(seu), copykat.test$prediction$cell.names) + seu$copykat.pred <- copykat.test$prediction$copykat.pred[idx] + + voi <- c('leiden_clusters','sctype_classification','lowConfidence_annot','copykat.pred') + final.obj$copykat.pred <- seu$copykat.pred + }else{ + voi <- c('leiden_clusters','sctype_classification','lowConfidence_annot') + } + + voi_df <- data.frame(FetchData(seu, vars = voi)) |> tibble::rownames_to_column(var = "barcode") + write.table(voi_df, sep = "\t", quote = F, row.names = F, + file = file.path(out_loc,"results",paste0(ind.lib,"_metadata.txt"))) + final.obj$sctype_classification <- seu$sctype_classification + final.obj$lowConfidence_annot <- seu$lowConfidence_annot + saveRDS(final.obj, file = file.path(out_loc,"results/rds",paste0(ind.lib,".rds"))) +} + + +project_root <- rprojroot::find_root(rprojroot::is_git_root) +projectID <- "SCPCP000003" +out_loc <- file.path(project_root, "analyses/cell-type-ETP-ALL-03") +data_loc <- file.path(project_root, "data/current",projectID) +dir.create(file.path(out_loc, "results/copykat_output"), showWarnings = FALSE) +setwd(file.path(out_loc, "results/copykat_output")) + +metadata <- read.table(file.path(data_loc,"single_cell_metadata.tsv"), sep = "\t", header = T) +metadata <- metadata[which(metadata$scpca_project_id == projectID & + metadata$diagnosis == "Early T-cell precursor T-cell acute lymphoblastic leukemia"), ] +libraryID <- metadata$scpca_library_id +# DB file +db <- file.path(out_loc,"Azimuth_BM_level1.csv") +tissue <- "Immune system" + +purrr::walk(libraryID, run_annot) diff --git a/analyses/cell-type-ETP-ALL-03/scripts/multipanel_plot.R b/analyses/cell-type-ETP-ALL-03/scripts/multipanel_plot.R new file mode 100644 index 000000000..dbdcce75f --- /dev/null +++ b/analyses/cell-type-ETP-ALL-03/scripts/multipanel_plot.R @@ -0,0 +1,48 @@ +#!/usr/bin/env Rscript + +#This script combines multiple UMAP plots from an individual library into one multi-panel plot + +library(Seurat) +library(ggplot2) + +multiplot <- function(annot.obj, library.id, ct.colors, n.row = 2, + variables.to.plot = c("leiden_clusters","sctype_classification","lowConfidence_annot","copykat.pred")){ + plot.list <- list() + for (plot.type in variables.to.plot){ + if (plot.type %in% c("sctype_classification","lowConfidence_annot")){ + clrs <- ct.colors + } else{ + clrs <- NULL + } + tryCatch({ + plot.list[[plot.type]] <- DimPlot(annot.obj, reduction = "Xumap_", group.by = plot.type, + label = T, cols = clrs, repel = T) + NoLegend() + }, error=function(e){}) + } + cowplot::plot_grid(plotlist = plot.list, nrow = n.row) + + cowplot::draw_figure_label(library.id, position = "top", size = 18, fontface = "bold") + ggsave(file.path(out_loc,"plots",paste0("multipanels_",library.id,".png")), width = 12, height = 12, bg = "white", dpi = 150) +} + +project_root <- rprojroot::find_root(rprojroot::is_git_root) +projectID <- "SCPCP000003" +out_loc <- file.path(project_root, "analyses/cell-type-ETP-ALL-03") +data_loc <- file.path(project_root, "data/current",projectID) + +metadata <- read.table(file.path(data_loc,"single_cell_metadata.tsv"), sep = "\t", header = T) +metadata <- metadata[which(metadata$scpca_project_id == projectID & + metadata$diagnosis == "Early T-cell precursor T-cell acute lymphoblastic leukemia"), ] +libraryID <- metadata$scpca_library_id + +ct_color <- c("darkorchid","skyblue2","dodgerblue2","gold","beige","sienna1","green4","navy", + "chocolate4","red","darkred","#6A3D9A","maroon","yellow4","grey35","black","lightpink","grey80") +names(ct_color) <- c("B","CD4 T","CD8 T","DC","HSPC","Mono","NK","Other T","Macrophage", + "Early Eryth","Late Eryth","Plasma","Platelet","Stromal","Blast","Cancer","Pre Eryth","Unknown") + +seu.list <- list() +for (lib_iter in 1:length(libraryID)){ + seu.list[[lib_iter]] <- readRDS(file.path(out_loc,"results/rds",paste0(libraryID[lib_iter],".rds"))) + names(seu.list)[lib_iter] <- libraryID[lib_iter] +} + +purrr::walk2(seu.list, names(seu.list), ~ multiplot (annot.obj = .x, library.id = .y, ct.colors = ct_color)) diff --git a/analyses/cell-type-nonETP-ALL-03/Dockerfile b/analyses/cell-type-nonETP-ALL-03/Dockerfile index d973dded8..dffa86a9b 100644 --- a/analyses/cell-type-nonETP-ALL-03/Dockerfile +++ b/analyses/cell-type-nonETP-ALL-03/Dockerfile @@ -6,7 +6,7 @@ FROM bioconductor/r-ver:3.19 LABEL org.opencontainers.image.title="openscpca/cell-type-nonETP-ALL-03" LABEL org.opencontainers.image.description="Docker image for the OpenScPCA analysis module 'cell-type-nonETP-ALL-03'" LABEL org.opencontainers.image.authors="OpenScPCA scpca@ccdatalab.org" -LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/templates/analysis-module" +LABEL org.opencontainers.image.source="https://github.com/AlexsLemonade/OpenScPCA-analysis/tree/main/analyses/cell-type-nonETP-ALL-03" # Set an environment variable to allow checking if we are in an OpenScPCA container ENV OPENSCPCA_DOCKER=TRUE