xgxofdream
commented
1 month ago 报错如下：
> setwd(MR_DIR); cat("当前工作目录：", getwd()) 当前工作目录： F:/0. MR_Project/03_MR_Basic/AhR(eqtl-a-ENSG00000106546)→DVT(ebi-a-GCST90038615)/5_do_MR> result_file <- file.path(MR_DIR, "MR-Result.csv") > pFilter <- 1 # 是否根据 P 值过滤？1：不过滤；0.05：过滤 > > draw_forest_map <- function(inputFile = null, forestFile = null, forestCol = null) { + # 读取输入文件 + rt <- read.csv(inputFile, header = T, sep = ",", check.names = F) + row.names(rt) <- rt$method + rt <- rt[rt$pval < pFilter,] + method <- rownames(rt) + or <- sprintf("%.3f", rt$"or") + orLow <- sprintf("%.3f", rt$"or_lci95") + orHigh <- sprintf("%.3f", rt$"or_uci95") + OR <- paste0(or, "(", orLow, "-", orHigh, ")") + pVal <- ifelse(rt$pval < 0.001, "<0.001", sprintf("%.3f", rt$pval)) + + #输出图形 + pdf(file = forestFile, width = 7, height = 4.6) + n <- nrow(rt) + nRow <- n + 1 + ylim <- c(1, nRow) + layout(matrix(c(1, 2), nc = 2), width = c(3.5, 2)) + + # 左侧 + xlim <- c(0, 3) + par(mar = c(4, 2.5, 2, 1)) + plot(1, xlim = xlim, ylim = ylim, type = "n", axes = F, xlab = "", ylab = "") + text.cex <- 0.8 + text(0, n:1, method, adj = 0, cex = text.cex) + text(1.9, n:1, pVal, adj = 1, cex = text.cex); text(1.9, n + 1, 'pvalue', cex = 1, font = 2, adj = 1) + text(3.1, n:1, OR, adj = 1, cex = text.cex); text(2.7, n + 1, 'OR', cex = 1, font = 2, adj = 1) + + # 右侧 + par(mar = c(4, 1, 2, 1), mgp = c(2, 0.5, 0)) + xlim <- c(min(as.numeric(orLow) * 0.975, as.numeric(orHigh) * 0.975, 0.9), max(as.numeric(orLow), as.numeric(orHigh)) * 1.025) + plot(1, xlim = xlim, ylim = ylim, type = "n", axes = F, ylab = "", xaxs = "i", xlab = "OR") + arrows(as.numeric(orLow), n:1, as.numeric(orHigh), n:1, angle = 90, code = 3, length = 0.05, col = "darkblue", lwd = 3) + abline(v = 1, col = "black", lty = 2, lwd = 2) + boxcolor <- ifelse(as.numeric(or) > 1, forestCol, forestCol) + points(as.numeric(or), n:1, pch = 15, col = boxcolor, cex = 2) + axis(1) + dev.off() + } > > draw_forest_map(inputFile = result_file, forestFile = "forest_map.pdf", forestCol = "red") Error in file(file, "rt") : 无法打开链结 Called from: file(file, "rt")
找到原因了。因为5_do_MR1.R没有运行完成并成功。
报错如下：