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

@@ -136,8 +136,7 @@ library(RColorBrewer)
     
 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="-")
+  colnames(seqtab) <- paste(taxtable[, 1], taxtable[, 2], taxtable[, 3], taxtable[, 4], taxtable[, 5], taxtable[, 6], as.character(1:length(taxtable[, 1])), sep="-")
   seqtab <- seqtab[, grep("Chloroplast|Mitochondria", colnames(seqtab), invert=TRUE)]
   seqtab <- seqtab/rowSums(seqtab)
   seqtab1 <- seqtab[, sapply(seqtab, function(x) max(x)) >= min_abund]
@@ -158,7 +157,8 @@ seqtab.m$Class <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 3)
   seqtab.m$Order <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 4)
   seqtab.m$Family <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 5)
   seqtab.m$Genus <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 6)
-seqtab.m <- cbind(seqtab.m, replicate(1,seqtab.m[colnames(seqtab.m) == taxonomicLevel]))
+  seqtab.m <- cbind(seqtab.m, replicate(1,seqtab.m[colnames(seqtab.m) == 
+taxonomicLevel]))
   colnames(seqtab.m) <- c(colnames(seqtab.m)[1:length(colnames(seqtab.m)) -1], "displayLevel")
   nb.cols <- length(seqtab) - 1
   mycolours <- rep(brewer.pal(12, "Paired"), ceiling(nb.cols/12))