| |
| |
| |
| |
|
|
| suppressPackageStartupMessages({ |
| library(dplyr) |
| library(ggplot2) |
| library(clusterProfiler) |
| library(AnnotationDbi) |
| try(library(org.Mm.eg.db), silent = TRUE) |
| try(library(org.Hs.eg.db), silent = TRUE) |
| }) |
|
|
| args <- commandArgs(trailingOnly = TRUE) |
| parse_arg <- function(name, default = NULL) { |
| idx <- grep(paste0("^--", name, "="), args) |
| if (length(idx) == 0) { |
| idx <- match(paste0("--", name), args) |
| if (!is.na(idx) && idx < length(args)) return(args[idx + 1]) |
| return(default) |
| } |
| sub(paste0("^--", name, "="), "", args[idx][1]) |
| } |
|
|
| deg_file <- parse_arg("deg") |
| output_csv <- parse_arg("output_csv") |
| output_pdf <- parse_arg("output_pdf") |
| species <- parse_arg("species", "Mm") |
| ontology <- parse_arg("ontology", "ALL") |
| pval_cutoff <- as.numeric(parse_arg("pval_cutoff", "0.05")) |
|
|
| if (is.null(deg_file) || is.null(output_csv) || is.null(output_pdf)) { |
| stop("Usage: Rscript 04_go_enrichment.R --deg=DEG.csv --output_csv=OUT.csv --output_pdf=OUT.pdf [--species=Mm] [--ontology=ALL] [--pval_cutoff=0.05]") |
| } |
|
|
| deg <- read.csv(deg_file, stringsAsFactors = FALSE) |
| ids <- deg %>% filter(Status %in% c("Up", "Down") & !is.na(ENTREZID)) %>% pull(ENTREZID) |
| ids <- as.character(unique(ids)) |
| bg_entrez <- deg %>% filter(!is.na(ENTREZID)) %>% pull(ENTREZID) %>% unique() %>% as.character() |
|
|
| if (length(ids) == 0) stop("无有效 ENTREZID") |
|
|
| db_pkg <- if (species == "Mm") "org.Mm.eg.db" else "org.Hs.eg.db" |
| if (!require(db_pkg, character.only = TRUE, quietly = TRUE)) stop("请安装 ", db_pkg) |
| db_obj <- get(db_pkg) |
|
|
| go_obj <- enrichGO( |
| gene = ids, |
| OrgDb = db_obj, |
| keyType = "ENTREZID", |
| ont = ontology, |
| pAdjustMethod = "BH", |
| pvalueCutoff = pval_cutoff, |
| qvalueCutoff = 0.2, |
| readable = TRUE, |
| universe = if (length(bg_entrez) > 0) bg_entrez else NULL |
| ) |
|
|
| if (is.null(go_obj) || nrow(go_obj@result) == 0) { |
| message("GO 富集无显著结果") |
| df_out <- data.frame(ID = character(), Description = character(), GeneRatio = character(), |
| BgRatio = character(), pvalue = numeric(), p.adjust = numeric(), qvalue = numeric(), |
| geneID = character(), Count = integer(), stringsAsFactors = FALSE) |
| } else { |
| df_out <- go_obj@result |
| df_out$Description <- gsub("\\s*\\(.*\\)$", "", df_out$Description) |
| } |
|
|
| dir.create(dirname(output_csv), recursive = TRUE, showWarnings = FALSE) |
| write.csv(df_out, output_csv, row.names = FALSE) |
| message("GO 结果已保存: ", output_csv) |
|
|
| if (nrow(df_out) > 0) { |
| df_plot <- head(df_out[order(df_out$p.adjust), ], 20) |
| df_plot$Count <- as.integer(sapply(strsplit(df_plot$GeneRatio, "/"), `[`, 1)) |
| df_plot$Description <- factor(df_plot$Description, levels = rev(df_plot$Description)) |
|
|
| p <- ggplot(df_plot, aes(x = Count, y = Description, size = Count, color = p.adjust)) + |
| geom_point() + |
| scale_color_gradient(low = "#e74c3c", high = "#3498db") + |
| labs(x = "Gene Count", y = "", color = "Adj.P", size = "Count") + |
| theme_bw(base_size = 10) + |
| theme(axis.text.y = element_text(size = 9)) |
| ggsave(output_pdf, p, width = 9, height = max(5, nrow(df_plot) * 0.25)) |
| message("GO 点图已保存: ", output_pdf) |
| } else { |
| pdf(output_pdf, width = 6, height = 4) |
| plot.new() |
| text(0.5, 0.5, "No significant GO enrichment", cex = 1.2) |
| dev.off() |
| } |
|
|
