#!/usr/bin/env Rscript
# ChatSpatial R Dependencies Installation Script
# This script installs all R packages required for ChatSpatial's R-based methods
#
# Usage:
# Rscript install_r_dependencies.R
# or in R console: source("install_r_dependencies.R")
cat("\n")
cat("========================================\n")
cat("ChatSpatial R Dependencies Installer\n")
cat("========================================\n\n")
# Set CRAN mirror
options(repos = c(CRAN = "https://cran.r-project.org"))
# Helper function to install package with error handling
install_if_missing <- function(pkg, source = "CRAN", install_cmd = NULL) {
cat(sprintf("Checking %s (%s)...", pkg, source))
if (require(pkg, character.only = TRUE, quietly = TRUE)) {
cat(" ✓ Already installed\n")
return(TRUE)
}
cat(" Installing...\n")
tryCatch({
if (!is.null(install_cmd)) {
eval(parse(text = install_cmd))
} else {
install.packages(pkg, quiet = FALSE)
}
# Verify installation
if (require(pkg, character.only = TRUE, quietly = TRUE)) {
cat(sprintf(" ✓ %s installed successfully\n", pkg))
return(TRUE)
} else {
cat(sprintf(" ✗ %s installation verification failed\n", pkg))
return(FALSE)
}
}, error = function(e) {
cat(sprintf(" ✗ Failed to install %s: %s\n", pkg, e$message))
return(FALSE)
})
}
# Track installation results
failed_packages <- c()
success_count <- 0
total_count <- 0
cat("\n")
cat("Step 1: Installing Base Dependencies\n")
cat("-------------------------------------\n")
# Install devtools (needed for GitHub packages)
total_count <- total_count + 1
if (install_if_missing("devtools", "CRAN")) {
success_count <- success_count + 1
} else {
failed_packages <- c(failed_packages, "devtools (CRAN)")
}
# Install BiocManager (needed for Bioconductor packages)
total_count <- total_count + 1
if (install_if_missing("BiocManager", "CRAN")) {
success_count <- success_count + 1
} else {
failed_packages <- c(failed_packages, "BiocManager (CRAN)")
}
cat("\n")
cat("Step 2: Installing CRAN Packages\n")
cat("---------------------------------\n")
cran_packages <- c(
"dplyr", # Data manipulation (required by scType, Numbat, CellChat)
"openxlsx", # Excel file reading (required by scType)
"HGNChelper", # Gene name validation (required by scType)
"SPARK", # Spatial variable genes (SPARK method)
"sctransform" # SCTransform v2 normalization (variance-stabilizing)
)
for (pkg in cran_packages) {
total_count <- total_count + 1
if (install_if_missing(pkg, "CRAN")) {
success_count <- success_count + 1
} else {
failed_packages <- c(failed_packages, paste0(pkg, " (CRAN)"))
}
}
cat("\n")
cat("Step 3: Installing Bioconductor Packages\n")
cat("-----------------------------------------\n")
bioc_packages <- list(
list(name = "SPOTlight", cmd = "BiocManager::install('SPOTlight', update = FALSE, ask = FALSE)")
)
for (pkg_info in bioc_packages) {
total_count <- total_count + 1
if (install_if_missing(pkg_info$name, "Bioconductor", pkg_info$cmd)) {
success_count <- success_count + 1
} else {
failed_packages <- c(failed_packages, paste0(pkg_info$name, " (Bioconductor)"))
}
}
cat("\n")
cat("Step 4: Installing GitHub Packages\n")
cat("-----------------------------------\n")
cat("Note: GitHub installations may take longer...\n\n")
github_packages <- list(
list(
name = "spacexr",
repo = "dmcable/spacexr",
method = "RCTD deconvolution",
cmd = "devtools::install_github('dmcable/spacexr', build_vignettes = FALSE, upgrade = 'never')"
),
list(
name = "CARD",
repo = "YingMa0107/CARD",
method = "CARD deconvolution",
cmd = "devtools::install_github('YingMa0107/CARD', upgrade = 'never')"
),
list(
name = "CellChat",
repo = "jinworks/CellChat",
method = "Cell-cell communication",
cmd = "devtools::install_github('jinworks/CellChat', upgrade = 'never')"
),
list(
name = "numbat",
repo = "kharchenkolab/numbat",
method = "CNV analysis",
cmd = "devtools::install_github('kharchenkolab/numbat', upgrade = 'never')"
)
)
for (pkg_info in github_packages) {
cat(sprintf("Installing %s (%s) from GitHub...\n", pkg_info$name, pkg_info$method))
total_count <- total_count + 1
if (install_if_missing(pkg_info$name, paste0("GitHub: ", pkg_info$repo), pkg_info$cmd)) {
success_count <- success_count + 1
} else {
failed_packages <- c(failed_packages, paste0(pkg_info$name, " (GitHub: ", pkg_info$repo, ")"))
}
}
# Print summary
cat("\n")
cat("========================================\n")
cat("Installation Summary\n")
cat("========================================\n")
cat(sprintf("Successfully installed: %d/%d packages\n", success_count, total_count))
if (length(failed_packages) > 0) {
cat("\n⚠️ Failed packages:\n")
for (pkg in failed_packages) {
cat(sprintf(" - %s\n", pkg))
}
cat("\n")
cat("Troubleshooting:\n")
cat("1. Check your internet connection\n")
cat("2. Update R to the latest version\n")
cat("3. Try installing failed packages manually\n")
cat("4. Check the ChatSpatial documentation for platform-specific instructions\n")
cat("\n")
} else {
cat("\n✓ All R dependencies installed successfully!\n\n")
cat("You can now use ChatSpatial's R-based methods:\n")
cat(" • RCTD deconvolution (spacexr)\n")
cat(" • SPOTlight deconvolution (SPOTlight)\n")
cat(" • CARD deconvolution (CARD)\n")
cat(" • CellChat cell communication (CellChat)\n")
cat(" • SCTransform normalization (sctransform)\n")
cat(" • scType cell type annotation (dplyr, openxlsx, HGNChelper)\n")
cat(" • Numbat CNV analysis (numbat)\n")
cat(" • SPARK spatial variable genes (SPARK)\n")
cat("\n")
}
# Print R session info for debugging
cat("R Session Information:\n")
cat("---------------------\n")
cat(sprintf("R version: %s\n", R.version.string))
cat(sprintf("Platform: %s\n", R.version$platform))
cat("\nInstallation complete!\n")
