ncm_fastq.py 文件源码

def generate_R_scripts():
    r_file = open(outdir + "/r_script.r","w")
    if len(feature_list)==0:
       r_file.close()
    else :
       cmd = "output_corr_matrix <- read.delim(\"" + outdir +  "/output_corr_matrix.txt\")\n"
       cmd = cmd + "data = output_corr_matrix\n"
       cmd = cmd + "d3 <- as.dist((1 - data[,-1]))\n"
       cmd = cmd + "clust3 <- hclust(d3, method = \"average\")\n"
       if len(feature_list) < 5:
           cmd = cmd + "pdf(\"" +outdir+ "/" + pdf_tag + ".pdf\", width=10, height=7)\n"
       else:
           cmd = cmd + "pdf(\"" +outdir+ "/" + pdf_tag + ".pdf\", width="+str(math.log10(len(feature_list))*10) +", height=7)\n"
       cmd = cmd + "op = par(bg = \"gray85\")\n"
       cmd = cmd + "par(plt=c(0.05, 0.95, 0.2, 0.9))\n"
       cmd = cmd + "plot(clust3, lwd = 2, lty = 1,cex=0.8, xlab=\"Samples\", sub = \"\",  ylab=\"Distance (1-Pearson correlation)\",hang = -1, axes = FALSE)\n"
       cmd = cmd + "axis(side = 2, at = seq(0, 1, 0.2), labels = FALSE, lwd = 2)\n"
       cmd = cmd + "mtext(seq(0, 1, 0.2), side = 2, at = seq(0, 1, 0.2), line = 1,   las = 2)\n"
       cmd = cmd + "dev.off()\n"
       r_file.write(cmd)
       r_file.close()