Practical-3-Processing-16S-rRNA-amplicon-data.md

@@ -111,13 +111,13 @@ For now though, we're just going to use a (relatively) simple plotting function
     library(reshape2)
     library(RColorBrewer)
     
-    plotTaxon <- function(seqtab, taxon, min_abund, taxonomicLevel) {
-      seqtab.copy <- seqtab
-      seqtab.copy <- data.frame(seqtab.copy)
-      colnames(seqtab.copy) <- paste(tax[, 1], tax[, 2], tax[, 3], tax[, 4], tax[, 5], tax[, 6], as.character(1:length(tax[, 1])), sep="-")
-      seqtab.copy <- seqtab.copy/rowSums(seqtab.copy)
-      seqtab.copy <- seqtab.copy[, sapply(seqtab.copy, function(x) max(x)) >= min_abund]
-      seqtab.copy$sample <- rownames(seqtab.copy)
+    plotTaxon <- function(seqtab, taxtable, taxon, min_abund, taxonomicLevel) {
+      seqtab <- data.frame(seqtab)
+      colnames(seqtab) <- paste(taxtable[, 1], taxtable[, 2], taxtable[, 3], taxtable[, 4], 
+taxtable[, 5], taxtable[, 6], as.character(1:length(taxtable[, 1])), sep="-")
+      seqtab <- seqtab/rowSums(seqtab)
+      seqtab <- seqtab[, sapply(seqtab, function(x) max(x)) >= min_abund]
+      seqtab$sample <- rownames(seqtab)
       seqtab.m <- melt(seqtab.copy)
       seqtab.m <- seqtab.m[grep(taxon, seqtab.m$variable),]
       seqtab.m$variable <- gsub("NA", "uncultured", seqtab.m$variable)
@@ -139,4 +139,4 @@ For now though, we're just going to use a (relatively) simple plotting function
         theme_classic() +
         theme(axis.text.x=element_text(angle=45, hjust=1))
     }
-    plotTaxon(seqtab, "Bacteroidetes", 0.01, "Genus")
+    plotTaxon(seqtab.nochim, taxa, "Bacteroidetes", 0.01, "Genus")