Nothing
## ---- echo = FALSE, message = FALSE, warning = FALSE---------------------
#knitr::opts_chunk$set(out.width='750px', dpi=200)
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", dpi=500, out.width='500px')
## ------------------------------------------------------------------------
data(woodmouse, package = "ape")
ape::as.character.DNAbin(woodmouse[1:5, 1:5])
## ------------------------------------------------------------------------
woodmouse <- woodmouse[, apply(woodmouse, 2, function(v) !any(v == 0xf0))]
## ------------------------------------------------------------------------
### Compute the full distance matrix and print the first few rows and columns
library(kmer)
woodmouse.kdist <- kdistance(woodmouse, k = 6)
print(as.matrix(woodmouse.kdist)[1:7, 1:7], digits = 2)
### Compute and print the embedded distance matrix
suppressWarnings(RNGversion("3.5.0"))
set.seed(999)
seeds <- sample(1:15, size = 3)
woodmouse.mbed <- mbed(woodmouse, seeds = seeds, k = 6)
print(woodmouse.mbed[,], digits = 2)
## ---- message = FALSE, fig.height=4, fig.width=10, fig.align='left', out.width= '700px'----
## compute pairwise distance matrices
dist1 <- ape::dist.dna(woodmouse, model = "K80")
dist2 <- kdistance(woodmouse, k = 7)
## build neighbor-joining trees
phy1 <- ape::nj(dist1)
phy2 <- ape::nj(dist2)
## rearrange trees in ladderized fashion
phy1 <- ape::ladderize(phy1)
phy2 <- ape::ladderize(phy2)
## convert phylo objects to dendrograms
dnd1 <- as.dendrogram(phy1)
dnd2 <- as.dendrogram(phy2)
## plot the tanglegram
dndlist <- dendextend::dendlist(dnd1, dnd2)
dendextend::tanglegram(dndlist, fast = TRUE, margin_inner = 5)
## ------------------------------------------------------------------------
suppressWarnings(RNGversion("3.5.0"))
set.seed(999)
woodmouse.OTUs <- otu(woodmouse, k = 5, threshold = 0.97, method = "farthest", nstart = 20)
woodmouse.OTUs
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.