File size: 2,459 Bytes
7e6a9d1 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 | #!/usr/bin/env Rscript
# =====================================================
# YuanSeq Snakemake - 火山图
# =====================================================
suppressPackageStartupMessages({
library(ggplot2)
library(dplyr)
})
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 <- parse_arg("output")
pval_cutoff <- as.numeric(parse_arg("pval_cutoff", "0.05"))
log2fc_cutoff <- as.numeric(parse_arg("log2fc_cutoff", "1"))
if (is.null(deg_file) || is.null(output)) {
stop("Usage: Rscript 02_volcano_plot.R --deg=DEG.csv --output=volcano.pdf [--pval_cutoff=0.05] [--log2fc_cutoff=1]")
}
deg <- read.csv(deg_file, stringsAsFactors = FALSE)
pval_col <- if ("padj" %in% colnames(deg)) "padj" else "pvalue"
deg <- deg %>%
mutate(
neglog10p = -log10(.data[[pval_col]]),
sig = case_when(
.data[[pval_col]] < pval_cutoff & log2FoldChange > log2fc_cutoff ~ "Up",
.data[[pval_col]] < pval_cutoff & log2FoldChange < -log2fc_cutoff ~ "Down",
TRUE ~ "NS"
)
)
label_col <- if ("SYMBOL" %in% colnames(deg) && !all(is.na(deg$SYMBOL))) "SYMBOL" else "GeneID"
top_n <- 20
deg_label <- deg %>%
filter(sig != "NS") %>%
arrange(desc(abs(log2FoldChange))) %>%
head(top_n)
p <- ggplot(deg, aes(x = log2FoldChange, y = neglog10p, color = sig)) +
geom_point(alpha = 0.6, size = 2) +
scale_color_manual(values = c(Up = "#e74c3c", Down = "#3498db", NS = "gray70")) +
geom_hline(yintercept = -log10(pval_cutoff), linetype = "dashed", color = "gray40") +
geom_vline(xintercept = c(-log2fc_cutoff, log2fc_cutoff), linetype = "dashed", color = "gray40") +
labs(x = "log2 Fold Change", y = paste0("-log10(", pval_col, ")"), color = "Status") +
theme_bw(base_size = 12) +
theme(legend.position = "top")
if (nrow(deg_label) > 0 && requireNamespace("ggrepel", quietly = TRUE)) {
p <- p + ggrepel::geom_text_repel(
data = deg_label,
aes(label = .data[[label_col]]),
size = 3,
max.overlaps = 20,
box.padding = 0.5
)
}
dir.create(dirname(output), recursive = TRUE, showWarnings = FALSE)
ggsave(output, p, width = 8, height = 6)
message("火山图已保存: ", output)
|