scpca-paper-figures

This repo contains the figures and tables included in the ScPCA manuscript.

Table of Contents

• Summary of figures and tables
• Generating figures and tables
• Sample info
• Color palettes
• Renv
• Contributing

Summary of figures and tables

Below is a summary of all figures and tables in the paper.

Figure 1

• A. Bar chart summarizing the types of diagnoses found on the Portal.
• B. Bar chart summarizing the types of modalities found on the Portal.
• C. Example project card as shown on the Portal.

Figure 2

• A. Overview of main workflow.
• B-G. Simplified versions of plots in the main QC report.

Figure 3

• A. Illustration of individual sample download folder.
• B. Illustration of merged project download folder.
• C. Overview of merged workflow.
• D. Example UMAPs found in merged report.

Figure 4

• A. Overview of cell type annotation workflow.
• B. Comparison of cell type annotations obtained using SingleR and CellAssign.

Supplemental Figure 1

• A. Comparison of run time and peak memory usage between Alevin-fry and Cell Ranger.
• B. Total UMI/cell between Alevin-fry and Cell Ranger.
• C. Total genes detected/cell between Alevin-fry and Cell Ranger.
• D. Correlation of mean gene expression between Alevin-fry and Cell Ranger.

Supplemental Figure 2

• A. Overview of cell type annotation workflow.
• B-D. Simplified versions of plots found in the ADT section of the main QC report.
• E. Overview of multiplexed library workflow.

Supplemental Figure 3

• A. Overview of bulk RNA-seq workflow.
• B. Overview of spatial transcriptomics workflow.

Supplemental Figure 4

Comparison of delta median statistic obtained from running SingleR with different celldex references.

Supplemental Figure 5

• A. UMAP displaying cell type annotations from CellAssign for an example ScPCA library.
• B. Heatmap comparing submitter provided annotations to CellAssign annotations for an example ScPCA library.

Supplemental Figure 6

• A. Diagnostic plot for cell type annotations from SingleR.
• B. Diagnostic plot for cell type annotations from CellAssign.

Supplemental Figure 7

Comparison between submitter provided annotations and automated annotations from SingleR and CellAssign.

Table S1

Summary of libraries and types of libraries found on the Portal.

Table S2

List of references used for each project on the Portal with CellAssign, including the list of organs used to create the reference.

Generating figures and tables

⚠️ This section currently requires internal Data Lab access to data

The figures and tables folders contain the most up-to-date version of each of the figures and tables, respectively. The scripts directory contains all scripts used to create the figures and tables. See the README for the scripts directory for more information on figure and table scripts.

To generate all figures and tables, run the script generate-figures-tables.sh as:

bash generate-figures-tables.sh

Note that this script assumes that the s3_files directory has been populated with relevant data files. These files can be obtained by first running the figure setup scripts, which currently require S3 bucket access as a Data Lab member. Setup scripts can be run as:

Rscript scripts/figure_setup/sync-metadata.R
Rscript scripts/figure_setup/sync-data-files.R
Rscript scripts/figure_setup/sync-reference-files.R

If you have setup 1Password to handle your AWS credentials, you will need to prefix those lines with op run --:

op run -- Rscript scripts/figure_setup/sync-metadata.R
op run -- Rscript scripts/figure_setup/sync-data-files.R
op run -- Rscript scripts/figure_setup/sync-reference-files.R

Sample info

The sample-info folder contains metadata files used to create figures and tables.

1. diagnosis-groupings.tsv: This tsv file contains one row per submitted_diagnosis associated with samples on the ScPCA Portal. For each submitted_diagnosis, a diagnosis_group is assigned.

2. disease-timing.tsv: This tsv file contains one row per submitted_disease_timing associated with samples on the ScPCA Portal. For each submitted_disease_timing, a standardized_disease_timing is assigned.

3. project-whiteliest.txt: This file contains a list of all projects that are currently active on the ScPCA Portal.

Color palettes

The palettes folder contains any palettes used in generating the figures.

1. diagnosis-group-palette.tsv: This is the palette used to color the diagnosis_group for each sample.
2. suspension-palette.tsv: This is the palette used to color libraries by Single-cell or Single-nuclei.
3. method-palette.tsv: This is the palette used to color by quantification method used, either Alevin-fry or Cell Ranger.

Manuscript numbers

The manuscript-numbers folder contains tables with total sample counts referenced when writing the manuscript. These tables are not included in the final manuscript and were created using scripts/Fig1A_sample-disease-barchart.R.

Renv

Package dependencies for scripts used in this repo are managed using renv. For renv to work as intended, you'll need to work within the scpca-paper-figures.Rproj project in RStudio. You may need to run renv::restore() upon opening the project to ensure the renv.lock file is synced with the project library.

Contributing

When developing new scripts, you may need to install or use new R packages. Each time you install or use new packages, you will want to run renv::snapshot() to update the renv.lock file with any added package and dependencies necessary to run the analyses and scripts in this repo.

In addition, this repository uses the parsable-r pre-commit hook to ensure R scripts are parsable. To use this hook, first ensure that that the pre-commit package is installed on your system; you can install it with your favorite method (pip install pre-commit or conda install pre-commit). Then, run pre-commit install in the scpca-paper-figures directory to enable pre-commit hooks in this repository. This will install the hooks in the .git/hooks directory, and they will be run automatically when you commit changes. If the hook fails, the commit will be aborted, and you will need to fix the errors and re-commit.