X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=rsem-plot-model;h=e87226d224a946109c60cc3821984ec9ba1793e8;hp=f7b84fc0e3664d5441807281afc2ad276aef4b8b;hb=83ce658a4b9c5f04c081316314b66b94ad5ffbde;hpb=58f823f5be6dfbe00896fc44ac3aac5e881e9c5c

diff --git a/rsem-plot-model b/rsem-plot-model
index f7b84fc..e87226d 100755
--- a/rsem-plot-model
+++ b/rsem-plot-model
@@ -2,15 +2,21 @@
 
 argv <- commandArgs(TRUE)
 if (length(argv) != 2) {
-  cat("Usage: rsem-plot-model sample_name outF\n")
+  cat("Usage: rsem-plot-model sample_name output_plot_file\n")
   q(status = 1)
 }
 
 strvec <- strsplit(argv[1], split = "/")[[1]]
 token <- strvec[length(strvec)]
 
-modelF <- paste(argv[1], ".stat/", token, ".model")
-cntF <- paste(argv[1], ".stat/", token, ".cnt")
+stat.dir <- paste(argv[1], ".stat", sep = "")
+if (!file.exists(stat.dir)) {
+  cat("Error: directory does not exist: ", stat.dir, "\n", sep = "")
+  cat(strwrap("This version of rsem-plot-model only works with the output of RSEM versions >= 1.1.8"), sep="\n")
+  q(status = 1)
+}
+modelF <- paste(stat.dir, "/", token, ".model", sep = "")
+cntF <- paste(stat.dir, "/", token, ".cnt", sep = "")
 
 pdf(argv[2])
 
@@ -27,7 +33,11 @@ x <- (vec[1] + 1) : vec[2]
 y <- as.numeric(strsplit(strvec[2], split = " ")[[1]])
 mean <- weighted.mean(x, y)
 std <- sqrt(weighted.mean((x - mean)^2, y))
-plot(x, y, type = "h", main = "Fragment Length Distribution", sub = paste("Mean = ", mean, ", Std = ", std), xlab = "Fragment Length", ylab = "Probability")  
+plot(x, y, type = "h",
+     main = "Fragment Length Distribution",
+     sub = paste("Mean = ", round(mean, 1), ", Std = ", round(std, 1)),
+     xlab = "Fragment Length",
+     ylab = "Probability")
 
 # mate length distribution
 if (model_type == 0 || model_type == 1) bval <- as.numeric(readLines(con, n = 1)[1]) else bval <- 1
@@ -40,7 +50,11 @@ if (bval == 1) {
   y <- as.numeric(list[[2]])
   mean <- weighted.mean(x, y)
   std <- sqrt(weighted.mean((x - mean)^2, y))
-  plot(x, y, type = "h", main = "Mate Length Distribution", sub = paste("Mean = ", mean, ", Std = ", std), xlab = "Mate Length", ylab = "Probability")  
+  plot(x, y, type = "h",
+       main = "Read Length Distribution",
+       sub=paste("Mean = ", round(mean, 1), ", Std = ", round(std, 1)),
+       xlab = "Read Length",
+       ylab = "Probability")
 }
 strvec <- readLines(con, n = 1)
 
@@ -65,32 +79,39 @@ if (model_type == 1 || model_type == 3) {
   # QProfile
   readLines(con, n = 1)
 
+  x <- c()
   peA <- c() # probability of sequencing error given reference base is A
   peC <- c()
   peG <- c()
   peT <- c()
-
+  
   for (i in 1 : N) {
     strvec <- readLines(con, n = 6)
     list <- strsplit(strvec[1:4], split = " ")
+
     vecA <- as.numeric(list[[1]])
     vecC <- as.numeric(list[[2]])
     vecG <- as.numeric(list[[3]])
     vecT <- as.numeric(list[[4]])
-    if (sum(c(vecA, vecC, vecG, vecT)) < 1e-8) break
-    peA <- c(peA, ifelse(sum(vec) < 1e-8, NA, -10 * log(1.0 - vecA[1])))
-    peC <- c(peC, ifelse(sum(vec) < 1e-8, NA, -10 * log(1.0 - vecC[2])))
-    peG <- c(peG, ifelse(sum(vec) < 1e-8, NA, -10 * log(1.0 - vecG[3])))
-    peT <- c(peT, ifelse(sum(vec) < 1e-8, NA, -10 * log(1.0 - vecT[4])))
+
+    if (sum(c(vecA, vecC, vecG, vecT)) < 1e-8) next
+    x <- c(x, (i - 1))
+    peA <- c(peA, ifelse(sum(vecA) < 1e-8, NA, -10 * log10(1.0 - vecA[1])))
+    peC <- c(peC, ifelse(sum(vecC) < 1e-8, NA, -10 * log10(1.0 - vecC[2])))
+    peG <- c(peG, ifelse(sum(vecG) < 1e-8, NA, -10 * log10(1.0 - vecG[3])))
+    peT <- c(peT, ifelse(sum(vecT) < 1e-8, NA, -10 * log10(1.0 - vecT[4])))
   }
 
-  x <- 0 : (length(peA) - 1)
-  matplot(x, cbind(peA, peC, peG, peT), type = "b", lty = 1:4, pch = 0:3, col = 1:4, main = "Quality Score vs. Observed Quality", xlab = "Quality Score", ylab = "Observed Quality")
+  matplot(x, cbind(peA, peC, peG, peT), type = "b", lty = 1:4, pch = 0:3, col = 1:4,
+          main = "Observed Quality vs. Phred Quality Score",
+          xlab = "Phred Quality Score",
+          ylab = "Observed Quality")
   legend("topleft", c("A", "C", "G", "T"), lty = 1:4, pch = 0:3, col = 1:4)
 } else {
   # Profile
   readLines(con, n = 1)
-  
+
+  x <- c()  
   peA <- c() # probability of sequencing error given reference base is A
   peC <- c()
   peG <- c()
@@ -99,18 +120,20 @@ if (model_type == 1 || model_type == 3) {
   for (i in 1: maxL) {
     strvec <- readLines(con, n = 6)
     list <- strsplit(strvec[1:4], split = " ")
+
     vecA <- as.numeric(list[[1]])
     vecC <- as.numeric(list[[2]])
     vecG <- as.numeric(list[[3]])
     vecT <- as.numeric(list[[4]])
-    if (sum(c(vecA, vecC, vecG, vecT)) < 1e-8) break
-    peA <- c(peA, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecA[1]) * 100))
-    peC <- c(peC, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecC[2]) * 100))
-    peG <- c(peG, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecG[3]) * 100))
-    peT <- c(peT, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecT[4]) * 100))
+
+    if (sum(c(vecA, vecC, vecG, vecT)) < 1e-8) next
+    x <- c(x, i)
+    peA <- c(peA, ifelse(sum(vecA) < 1e-8, NA, (1.0 - vecA[1]) * 100))
+    peC <- c(peC, ifelse(sum(vecC) < 1e-8, NA, (1.0 - vecC[2]) * 100))
+    peG <- c(peG, ifelse(sum(vecG) < 1e-8, NA, (1.0 - vecG[3]) * 100))
+    peT <- c(peT, ifelse(sum(vecT) < 1e-8, NA, (1.0 - vecT[4]) * 100))
   }
 
-  x <- 1 : length(peA)
   matplot(x, cbind(peA, peC, peG, peT), type = "b", lty = 1:4, pch = 0:3, col = 1:4, main = "Position vs. Percentage Sequence Error", xlab = "Position", ylab = "Percentage of Sequencing Error")
   legend("topleft", c("A", "C", "G", "T"), lty = 1:4, pch = 0:3, col = 1:4)       
 }
@@ -118,6 +141,9 @@ if (model_type == 1 || model_type == 3) {
 close(con)
 
 pair <- read.table(file = cntF, skip = 3, sep = "\t")
-plot(pair[,1], pair[,2], xlab = "Number of Alignments", ylab = "Number of Reads", main = "Among alignable reads, distribution of # of alignments")
+barplot(pair[,2], names.arg = pair[,1],
+        xlab = "Alignments per fragment",
+        ylab = "Number of fragments",
+        main = "Histogram of Alignments per Fragment")
 
-dev.off()
+dev.off.output <- dev.off()