01loadPackages.r

## 本脚本涉及环境
# BasicR = 4.4.3      ## 不建议在这个环境运行脚本
# irGSEA = 4.5.3
# monocle3_R4.5.2 = 4.5.2


# 第一步：先加载Bioconductor核心包（单独加载，不嵌套suppressMessages）
# 先指定库路径，避免多路径冲突
irGSEA_lib <- "/data/med-hancs/apps/anaconda3/2022.10/envs/irGSEA/lib/R/library"
BasicR_lib <- "/data/med-hancs/apps/anaconda3/2022.10/envs/BasicR/lib/R/library"
Monocle_lib <- "/data/med-hancs/apps/anaconda3/2022.10/envs/monocle3_R4.5.2/lib/R/library"
.libPaths(c(.libPaths(), BasicR_lib, Monocle_lib, irGSEA_lib)) # 统一库路径优先级

### 运行脚本前必须先加载系统模块
# module load hdf5/1.10.4-gcc-4.8.5       ## 主要是Azimuth需要

# 这里添加检测运行环境
env_nm <- Sys.getenv("CONDA_DEFAULT_ENV")
cat(paste0("当前运行环境: ",env_nm, "\n"))

# 这里添加检测R版本
#R_ver <- paste(R.version$major,R.version$minor,sep=".")
R_ver <- getRversion()
cat(paste0("当前R版本: ",R_ver, "\n"))

# 获取当前运行环境的安装包需要最低R版本 [这里可以再改进一点，获取所有环境的R包版本，分sheet记录]
pkgs <- installed.packages()
df <- data.frame(包名 = rownames(pkgs),
                 版本 = pkgs[, "Version"],
                 依赖R版本 = pkgs[, "Depends"],
                 建议R版本 = pkgs[, "Suggests"],
                 内置路径 = pkgs[, "LibPath"])
# 导出表格
write.csv(df, paste0("环境",env_nm,"_R包版本依赖清单.csv"), row.names = F)


pkgs <- c(
  # 基础核心
  "BiocGenerics","Biobase","Matrix","S4Vectors","IRanges","SummarizedExperiment","proxy",
  "Rcpp","future","furrr","optparse","getopt","pacman","scuttle","parallel","openxlsx",
  
  # 数据处理
  "tidyverse","data.table","reshape2","plyr","readxl","rhdf5","rjson","qs", #"scran",
  
  # 单细胞核心
  "sctransform","COSG","hdf5r", # "SeuratObject", "Seurat", "SeuratWrappers",
  "DropletUtils","SoupX","harmony","DoubletFinder","scCustomize","SingleCellExperiment",
  
  # 绘图可视化
  "ggplot2","cowplot","ggrepel","patchwork","ggridges","scater","maser","ggvenn",      # "ggbreak",
  "viridis","ggpubr","ggsci","ggrastr","pheatmap","corrplot","ROCR","igraph",
  
  # 统计分析
  "relaimpo","variancePartition","partR2","clinfun","MuMIn","entropy","ARTool",
  "DirichletReg","GeneNMF","Hmisc","fields","R.utils","RColorBrewer","pls","rdacca.hp",
  "ghp","fastDummies","car","broom","reformulas","DESeq2",
  
  # 注释&富集
  "biomaRt","AnnotationDbi","GenomicRanges","GenomicFeatures","txdbmaker","ensembldb",
  "org.Mm.eg.db","org.Hs.eg.db","org.Rn.eg.db","TxDb.Hsapiens.UCSC.hg38.knownGene",
  "TxDb.Rnorvegicus.UCSC.rn6.refGene","rtracklayer","Azimuth","KEGG.db","createKEGGdb",
  "clusterProfiler","enrichplot","msigdbr","ReactomePA","topGO","simplifyEnrichment",
  "fgsea","qusage","KEGGREST","GSEABase","BioNet","ggupset","ComplexHeatmap",
  
  # 细胞分型
  "MAST","AUCell","SingleR","UCell","SeedMatchR"
)

# 静默批量加载
invisible(suppressMessages(lapply(pkgs, library, character.only=TRUE, quietly=TRUE)))

# ===================== 4. 环境专用包（最后加载） =====================
if(env_nm == "monocle3_R4.5.2") library(monocle3, quietly=TRUE)
if(env_nm == "irGSEA") library(irGSEA, quietly=TRUE)

message("✅ 所有包加载完成，无任何依赖冲突！")