## load the dataset
data(FluH1N1pdm2009)
## create obkData object
x <- new("obkData", individuals = FluH1N1pdm2009$individuals, samples = FluH1N1pdm2009$samples,
dna = FluH1N1pdm2009$dna, trees = FluH1N1pdm2009$trees)
## first simple tree
p <- plotggphy(x, ladderize = TRUE)
## build tip attribute and use sample dates to scale the x-axis as date time
p <- plotggphy(x, ladderize = TRUE, build.tip.attribute = TRUE, branch.unit = "year",
tip.dates = "date")
## alternatively extract sample dates from the tip labels
p <- plotggphy(x, ladderize = TRUE, branch.unit = "year", guess.tip.dates.from.labels = TRUE,
set.guess = list(prefix = "_", order = 1, from = "last"))
## change x breaks and labels
p <- plotggphy(x, ladderize = TRUE, build.tip.attribute = TRUE, branch.unit = "year",
tip.dates = "date", major.breaks = "month", axis.date.format = "%b%Y")
## color-code tip location
p <- plotggphy(x, ladderize = TRUE, build.tip.attribute = TRUE, branch.unit = "year",
tip.dates = "date", tip.colour = "location")
## change tip size and transparency
p <- plotggphy(x, ladderize = TRUE, build.tip.attribute = TRUE, branch.unit = "year",
tip.dates = "date", tip.colour = "location", tip.size = 3, tip.alpha = 0.75)
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