assoc_repseq_IDs_with_otus_by_clstr <-
function(clstr_file, rep_seqs, otu_format="R") {
clstr.file <- read.table(file=clstr_file, stringsAsFactors=FALSE, header=FALSE, sep="\t", fill=TRUE)
# Create empty data frame of proper dimensions.
my.table <- matrix(0, length(rep_seqs), ncol=4)
my.table <- as.data.frame(my.table)
colnames(my.table) <- c("RepSeq.ID", "Cluster #", "Sample","Sequences in Sample")
# Fill in the table. Takes a while.
for (i in (1:length(rep_seqs))){
j <- grep(rep_seqs[i], clstr.file[,4], fixed=TRUE)
my.row <- c(rep_seqs[i], clstr.file[j,1:3])
my.row <- unlist(my.row)
my.table[i,] <- my.row
}
# Set proper classes for each column
i <- c(TRUE, FALSE, TRUE, FALSE)
my.table[i] <- lapply(my.table[i], as.character)
i <- c(FALSE, TRUE, FALSE, TRUE)
my.table[i] <- lapply(my.table[i], as.numeric)
# Add column of OTU names.
my.table$OTU <- make_otu_names(my.table[,2], otu_format)
my.table <- my.table[, c(1,5,2,3,4)]
i <- c(F,T,F,F,F)
my.table[i] <- lapply(my.table[i], as.character)
return(my.table)
}
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