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Updated Practical 3 Processing 16S rRNA amplicon data (markdown) authored by Ben Francis's avatar Ben Francis
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Practical-3-Processing-16S-rRNA-amplicon-data.md
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...@@ -157,8 +157,7 @@ plotTaxon <- function(seqtab, taxtable, taxon, min_abund, taxonomicLevel) { ...@@ -157,8 +157,7 @@ plotTaxon <- function(seqtab, taxtable, taxon, min_abund, taxonomicLevel) {
seqtab.m$Order <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 4) seqtab.m$Order <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 4)
seqtab.m$Family <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 5) seqtab.m$Family <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 5)
seqtab.m$Genus <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 6) seqtab.m$Genus <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 6)
seqtab.m <- cbind(seqtab.m, replicate(1,seqtab.m[colnames(seqtab.m) == seqtab.m <- cbind(seqtab.m, replicate(1,seqtab.m[colnames(seqtab.m) == taxonomicLevel]))
taxonomicLevel]))
colnames(seqtab.m) <- c(colnames(seqtab.m)[1:length(colnames(seqtab.m)) -1], "displayLevel") colnames(seqtab.m) <- c(colnames(seqtab.m)[1:length(colnames(seqtab.m)) -1], "displayLevel")
nb.cols <- length(seqtab) - 1 nb.cols <- length(seqtab) - 1
mycolours <- rep(brewer.pal(12, "Paired"), ceiling(nb.cols/12)) mycolours <- rep(brewer.pal(12, "Paired"), ceiling(nb.cols/12))
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