Fix bug in R plotting script

src/IMP_visualize_MGMT.R

@@ -159,9 +159,23 @@ annot <- readGff3(annot_file, isRightOpen = FALSE)
 
 # extract only interesting information
 print("Processing gff3 annotation file")
-annot.1 <- as.data.frame(cbind(as.character(annot@annotation$seq_name), annot@.Data,
-      str_split_fixed(str_split_fixed(getGffAttribute(annot, "inference"), ",", 2)[,2], ":", 3)[,2]))
+annot.1 <- as.data.frame(
+			 cbind(
+			       as.character(annot@annotation$seq_name), 
+			       annot@.Data,
+			       str_split_fixed(str_split_fixed(
+							       getGffAttribute(annot, "inference"), 
+							       ",", 2)[,2], ":", 3)[,2]
+			       )
+			 )
+
 colnames(annot.1) <- c("contig", "start", "end", "database")
+
+# Remove rows with no start and stop positions
+annot.1 <- annot.1[-is.na(annot.1$start),]
+annot.1 <- annot.1[-is.na(annot.1$end),]
+
+# Replace non-annotated gens with NA
 annot.1$database[annot.1$database==""]=NA
 
 annot.1[,2:3] <- sapply(annot.1[2:3], as.character)
@@ -172,6 +186,7 @@ print("Calculating no. of genes per contig")
 annot.2 <- as.data.frame(table(annot.1$contig))
 colnames(annot.2)[1:ncol(annot.2)] <- c("contig","no_of_genes")
 
+save.image()
 # calculate gene lengths
 print("Calculating length of genes from gff3 file")
 annot.1 <- as.data.frame(cbind(annot.1, annot.1$end - annot.1$start + 1))
@@ -179,8 +194,16 @@ colnames(annot.1)[ncol(annot.1)] <- "gene_length"
 
 # aggregate table and calculate total gene lengths within contig
 print("Calculating coding density of contigs")
-annot.2 <- cbind(annot.2, aggregate(gene_length~contig, data=annot.1, FUN=sum)[,2])
-colnames(annot.2)[ncol(annot.2)] <- "total_gene_length"
+# Create temporary table
+total_gene_length <- aggregate(gene_length~contig, data=annot.1, FUN=sum)
+colnames(total_gene_length)[ncol(total_gene_length)] <- "total_gene_length"
+annot.2 <- merge(annot.2, 
+		 total_gene_length,
+		 by="contig", 
+		 all.y=FALSE)
+
+# remove temporary table
+rm(total_gene_length)
 
 # create annotation table
 print("Creating annotation table")