added dockerfile

Author: rela-v

Dockerfile

@@ -0,0 +1,29 @@
+# 1. Use r-ver for native Apple Silicon (ARM64) support
+FROM rocker/r-ver:latest
+
+# 2. Install system dependencies + Pandoc (Critical for RMarkdown)
+RUN apt-get update && apt-get install -y \
+    libxml2-dev \
+    libssl-dev \
+    pandoc \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /project
+
+# 3. Setup renv files
+COPY renv.lock .Rprofile ./
+COPY renv/activate.R renv/activate.R
+RUN mkdir -p renv library data
+
+# 4. SPEED BOOST: 
+# - Use 'jammy' binaries (pre-compiled for the container's Ubuntu base)
+# - Use all CPU cores (Ncpus) to install 200+ packages in parallel
+RUN R -e "options(repos = c(CRAN = 'https://packagemanager.posit.co/cran/__linux__/jammy/latest'), Ncpus = parallel::detectCores()); renv::restore()"
+
+# 5. Copy your Rmd files and site configuration
+# Use a wildcard for _site.yml so it doesn't crash if the file is missing
+COPY *.Rmd ./
+COPY _site.ym[l] ./ 
+
+# 6. Render the site
+CMD ["R", "-e", "rmarkdown::render_site()"]

chapters/02-degs.Rmd

@@ -26,6 +26,12 @@ These are volcano plots of the DEGs.
 
 ```{r degs-volcanoplots, results="asis"}
 # Dynamically generate volcano plots for each data set
+# Load the configuration (usually at the start of your index.Rmd or setup chunk)
+config <- yaml::read_yaml("configuration.yml")
+
+# Access the toggle
+show_fdr <- config$use_fdr
+
 global_state$data %>%
   purrr::map(~ {
     # Create a new environment for each child
@@ -43,7 +49,7 @@ global_state$data %>%
         '',
         '```{r, echo=FALSE}',
         'if (has_data) {',
-        '  volcano_plot(current_data)',
+        '  volcano_plot(current_data, show_fdr)',
         '} else {',
         '  cat("No significant data available to display for this comparison.")',
         '}',

configuration.yml

@@ -1,6 +1,10 @@
 # For instructions on configuring the report see the README
 species: human # [human, rat, mouse]
 gmt: Human_GOALL_with_GO_iea_March_01_2025_symbol.gmt # [Human, Rat, Mouse]
+
+# Statistical Options
+use_fdr: true # [true, false] Set to true to show FDR line, false for raw p-value
+
 data:
   - group1: DA
     group2: CA