Compositional

.github/workflows/run_propeller.yml

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+name: Propeller compositional analysis
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - '04_compositional/propeller.qmd'
+  pull_request:
+    branches: [main]
+    paths:
+      - '04_compositional/propeller.qmd'
+  workflow_dispatch:
+
+jobs:
+  r-propeller:
+    runs-on: ubuntu-22.04
+
+    env:
+      RENV_PATHS_ROOT: ~/.local/share/renv  # persistent cache location
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install pandoc
+        run: sudo apt-get update && sudo apt-get install -y pandoc
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Install system dependencies for R packages
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libmagick++-dev libharfbuzz-dev libfribidi-dev libglpk-dev
+        shell: bash
+
+      - name: Cache R packages (renv)
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.RENV_PATHS_ROOT }}
+          key: ${{ runner.os }}-renv-${{ hashFiles('04_compositional/renv.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-renv-
+
+      - name: Set repositories
+        run: Rscript ubuntu.R
+
+      - name: Restore environment from renv.lock
+        run: |
+          install.packages("renv", repos = "https://cloud.r-project.org")
+          renv::restore(prompt = FALSE, lockfile = "04_compositional/renv.lock")
+        shell: Rscript {0}
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Run propeller report
+        id: render_qmd
+        run: |
+          cd 04_compositional
+          quarto render propeller.qmd
+        shell: bash
+
+      - name: Deploy HTML to gh-pages
+        if: success()
+        run: |
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git fetch origin gh-pages || git checkout --orphan gh-pages
+          git switch gh-pages || git checkout -b gh-pages
+          git add 04_compositional/propeller.html
+          git commit -m "Deploy propeller.html [skip ci]" || echo "No changes to commit"
+          git push origin gh-pages
+        shell: bash

04_compositional/propeller.qmd

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+---
+title: "Celltype composition with Propeller"
+author: "Harvard Chan Bioinformatics Core"
+date: "`r Sys.Date()`"
+format:
+   html:
+    number-sections: false
+    default-image-extension: svg
+    lightbox: true
+    callout-icon: false
+    format-links: true
+    toc: true
+    theme: sandstone
+    echo: true
+    eval: true
+    message: false
+    warning: false
+    code-copy: true
+    code-overflow: wrap
+    code-fold: true
+    code-line-numbers: true
+    embed-resources: true
+    standalone: true
+    html-math-method: katex
+    grid:
+      sidebar-width: 250px
+      body-width: 900px
+      margin-width: 300px
+    comments:
+      hypothesis: true
+params:
+   project_file: ../information.R
+knitr:
+  opts_chunk:
+    audodep: true
+    cache: false
+    cache.lazy: false
+    error: true
+    echo: false
+    fig-height: 5
+    fig.retina: 2
+    fig-width: 11
+    message: false
+    tidy: true
+    warning: false
+---
+
+```{r }
+#| message: false
+#| warning: false
+stopifnot(R.version$major >= 4) # requires R4
+if (compareVersion(R.version$minor, "3.1") < 0) warning("We recommend >= R4.3.1")
+stopifnot(compareVersion(as.character(BiocManager::version()), "3.18") >= 0)
+stopifnot(compareVersion(as.character(packageVersion("Seurat")), "5.0.0") >= 0)
+```
+
+This code is in this ![](https://img.shields.io/badge/status-draft-grey) revision.
+
+
+```{r setup}
+#| cache: false
+#| message: false
+#| warning: false
+#| echo: false
+# knitr::opts_chunk$set(echo = TRUE)
+# Load libraries
+library(knitr)
+library(rmarkdown)
+
+library(Seurat)
+library(SummarizedExperiment)
+library(SingleCellExperiment)
+library(DEGreport)
+library(pheatmap)
+library(limma)
+
+library(tidyverse)
+library(data.table)
+library(DT)
+library(patchwork)
+
+library(ggprism)
+library(grafify)
+
+library(future)
+library(speckle)
+# Set seed for reproducibility
+set.seed(1454944673L)
+
+ggplot2::theme_set(theme_prism(base_size = 12))
+# https://grafify-vignettes.netlify.app/colour_palettes.html
+# NOTE change colors here if you wish
+scale_colour_discrete <- function(...) {
+  scale_colour_manual(..., values = as.vector(grafify:::graf_palettes[["kelly"]]))
+}
+
+if (future::supportsMulticore()) {
+  future::plan(future::multicore)
+} else {
+  future::plan(future::multisession)
+}
+```
+
+```{r sanitize_datatable}
+sanitize_datatable <- function(df, ...) {
+  # remove dashes which cause wrapping
+  DT::datatable(df, ...,
+    rownames = gsub("-", "_", rownames(df)),
+    colnames = gsub("-", "_", colnames(df)),
+    options = list(scrollX = TRUE, ...)
+  )
+}
+```
+
+## Load object and subset
+Read in the full dataset Seurat object and subset to keep only cells from the conditions of interest (cold7 vs TN).
+
+```{r load-data}
+library(sccomp)
+data("seurat_obj")
+subset_seurat <- subset(x = seurat_obj, subset = sample %in% c("10x_6K", "SCP424_pbmc1", "SI-GA-G6", "SI-GA-H3"))
+Idents(object = subset_seurat) <- "cell_group"
+DefaultAssay(subset_seurat) <- "RNA"
+
+# Create metadata df and factor celltype
+meta <- subset_seurat@meta.data
+meta$cell_group <- factor(meta$cell_group)
+```
+
+## Check count numbers of cells
+
+```{r cellnumbers}
+meta$type_sample <- paste0(meta$type, "_", meta$sample)
+table(meta$type_sample, meta$cell_group)
+```
+
+## Run propeller
+
+```{r run-propeller}
+# working code; takes into account cell numbers
+# NOTE adapt with your variables of interest
+propres <- propeller(subset_seurat,
+  sample = subset_seurat$sample,
+  clusters = subset_seurat$cell_group,
+  group = subset_seurat$type
+)
+
+sanitize_datatable(propres)
+```
+
+## Proportions of cells table
+
+To understand discordance with sccomp results, let's evaluate proportions and variability within group. 
+
+
+```{r}
+props <- getTransformedProps(meta$cell_group,
+  meta$type_sample,
+  transform = "logit"
+)
+
+props$Proportions
+```
+
+```{r extracode}
+#| eval: false
+meta_propeller <- meta %>%
+  group_by(type, sample) %>%
+  distinct(sample)
+
+designAS <- model.matrix(~ meta_propeller$type)
+colnames(designAS) <- c("cancer", "healthy")
+
+fit <- lmFit(props$TransformedProps, designAS)
+fit <- eBayes(fit, robust = TRUE)
+
+topTable(fit)
+```
+# Resources
+
+* [Speckle vignette](http://127.0.0.1:29356/library/speckle/doc/speckle.html#finding-significant-differences-in-cell-type-proportions-using-propeller)
+* [Application to mouse PBMC scRNA](https://phipsonlab.github.io/propeller-paper-analysis/RealDataAnalysis.html#Young_vs_Old)
+
+# Conclusion
+
+# R session
+
+List and version of tools used for the QC report generation.
+
+```{r}
+sessionInfo()
+```
+
+