library(MotifBinner) library(ggplot2) library(ape) consensuses <- report_dat$pb_dat$consensuses
print(length(consensuses))
non_acgt <- NULL for (i in seq_along(consensuses)){ x <- sum(consensusMatrix(DNAStringSet(consensuses[[i]]))[-(1:4),]) non_acgt <- c(non_acgt, x) } barplot(table(non_acgt)) print(table(non_acgt))
dmat <- fast_stringDist(consensuses, 5) tot_dist <- apply(as.matrix(dmat), 1, sum) hist(tot_dist)
x <- pcoa(dmat) biplot(x)
normal_ranks <- rank(tot_dist) normal_ranks <- normal_ranks[order(normal_ranks)] rank_comp <- data.frame(seq_name = names(normal_ranks), normal_rank = normal_ranks, normal_dist = tot_dist[match(names(normal_ranks), names(tot_dist))]) row.names(rank_comp) <- 1:nrow(rank_comp) kable(head(rank_comp, 25)) kable(tail(rank_comp, 25))
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