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share/2_mash.tt2.sh  view on Meta::CPAN

        tmp <- as.matrix(tmp)
        mat <- tmp[,-1]
        rownames(mat) <- tmp[,1]

        dist_mat <- as.dist(mat)
        clusters <- hclust(dist_mat, method = "ward.D2")
        tree <- as.phylo(clusters)
        write.tree(phy=tree, file="tree.nwk")

        group <- cutree(clusters, h=0.4) # k=5
        groups <- as.data.frame(group)
        groups$ids <- rownames(groups)
        rownames(groups) <- NULL
        groups <- groups[order(groups$group), ]
        write_tsv(groups, "groups.tsv")
    '

log_info newick-utils
cat tree.nwk |
[% IF opt.outgroup -%]
    nw_reroot - [% opt.outgroup %] |

share/plot_tree.R  view on Meta::CPAN

        font = 1,
        adj = 0,
        xpd = TRUE,
        label.offset = 0.001,
        no.margin = TRUE,
        underscore = TRUE
    )
    nodelabels(
        tree$node.label,
        adj = c(1.3,-0.5),
        frame = "n",
        cex = 0.8,
        font = 3,
        xpd = TRUE
    )
    add.scale.bar(cex = 0.8, lwd = 2, length = barlen)
}

pdf(file = opt$outfile)
tree <- read.tree(opt$infile)
plot_tree(tree)