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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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...@@ -139,11 +139,17 @@ then do the plotting :) ...@@ -139,11 +139,17 @@ then do the plotting :)
taxtable[, 5], taxtable[, 6], as.character(1:length(taxtable[, 1])), sep="-") taxtable[, 5], taxtable[, 6], as.character(1:length(taxtable[, 1])), sep="-")
seqtab <- seqtab[, grep("Chloroplast|Mitochondria", colnames(seqtab), invert=TRUE)] seqtab <- seqtab[, grep("Chloroplast|Mitochondria", colnames(seqtab), invert=TRUE)]
seqtab <- seqtab/rowSums(seqtab) seqtab <- seqtab/rowSums(seqtab)
seqtab <- seqtab[, sapply(seqtab, function(x) max(x)) >= min_abund] seqtab1 <- seqtab[, sapply(seqtab, function(x) max(x)) >= min_abund]
seqtab2 <- seqtab[, sapply(seqtab, function(x) max(x)) < min_abund]
colnames(seqtab2) <- paste0(colnames(seqtab2), "_Others")
seqtab3 <- merge(seqtab1, seqtab2, by="row.names")
row.names(seqtab3) <- row.names(seqtab)
seqtab <- seqtab3
seqtab$sample <- rownames(seqtab) seqtab$sample <- rownames(seqtab)
seqtab.m <- melt(seqtab) seqtab.m <- melt(seqtab)
seqtab.m <- seqtab.m[grep(taxon, seqtab.m$variable),] seqtab.m <- seqtab.m[grep(taxon, seqtab.m$variable),]
seqtab.m$variable <- gsub("NA", "uncultured", seqtab.m$variable) seqtab.m$variable <- gsub("NA", "uncultured", seqtab.m$variable)
seqtab.m$variable <- gsub(".*Others", "Below_Min_Abund-Below_Min_Abund-Below_Min_Abund-Below_Min_Abund-Below_Min_Abund-Below_Min_Abund-Below_Min_Abund", seqtab.m$variable)
seqtab.m$variable <- as.character(seqtab.m$variable) seqtab.m$variable <- as.character(seqtab.m$variable)
seqtab.m$Domain <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 1) seqtab.m$Domain <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 1)
seqtab.m$Phylum <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 2) seqtab.m$Phylum <- sapply(strsplit(seqtab.m$variable, "-"), "[[", 2)
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