plotggphy: Function to plot phylogenies using 'ggplot2'
In thibautjombart/OutbreakTools: Basic Tools for the Analysis of Disease Outbreaks

Description Usage Arguments Author(s) Examples

Function to plot phylogenies using ggplot2

  plotggphy(x, which.tree = 1, ladderize = TRUE,
    show.tip.label = NULL, tip.label.size = 3,
    build.tip.attribute = TRUE, tip.color = NULL,
    tip.alpha = NULL, tip.shape = NULL, tip.size = NULL,
    branch.unit = NULL, tip.dates = NULL,
    guess.tip.dates.from.labels = FALSE,
    set.guess = list(prefix = "_", order = 1, from = "last"),
    axis.date.format = NULL, major.breaks = NULL,
    minor.breaks = NULL, color.palette = "Spectral",
    legend.position = "right")

`x`	An obkData object.
`which.tree`	Numeric. Specify the order of the tree to be plotted. Currently the function cannot plot multiple tree.
`ladderize`	If `TRUE`, the phylogeny is ladderized
`show.tip.label`	Logical. If `TRUE`, the labels of the tip are shown; if `NULL` (default), labels are shown for tree sizes up to 50 tips.
`tip.label.size`	Numeric. Size of the tip labels.
`build.tip.attribute`	Logical. If `TRUE`, then a data frame `tip.attribute` is constructed by merging the data frames `individuals` and `samples`.
`tip.color`	Character. Can be either the name of a color (e.g. "Black") or the name of a column of `tip.attribute`. In the first case, all tips have the specified color. In the second case, tips are color-codded according to the specified attribute.
`tip.alpha`	Character (or Numeric). Can be either the value of transparency (between 0 and 1) or the name of a column of `tip.attribute`. In the first case, all tips have the specified transparency. In the second case, tips are transparency-codded according to the specified attribute.
`tip.shape`	Character (or Numeric). Can be either the value of a shape (e.g. 16 correpond to filled circles) or the name of a column of `tip.attribute`. In the first case, all tips have the specified shape. In the second case, tips are shape-codded according to the specified attribute.
`tip.size`	Character (or Numeric). Can be either the value of tip size or the name of a column of `tip.attribute`. In the first case, all tips have the specified size. In the second case, tips are size-codded according to the specified attribute.
`branch.unit`	Character. The unit of the branch can be either "year", "month", "day" or "subst". If a time unit is provided, together with use.tip.dates, then the x-axis of the phylogeny is plotted in date format using standard POSIX specification.
`tip.dates`	Character. If branch.unit is in unit of time, tip.dates indicates the name of the column of tip.attribute that contains the sampling dates of the tip. See also guess.tip.dates.from.labels.
`guess.tip.dates.from.labels`	Logical. If `TRUE` then tip.dates are guessed from the tip labels using the information provided by 'set.guess'.
`set.guess`	List. A list of three elements: prefix, order and from. For instance, if labels are formated like this: A/Shenzhen/40/2009_China_2009-06-09 then set.guess = list(prefix="_",order=3,from="first") or set.guess = list(prefix="_",order=1,from="last").
`axis.date.format`	Character. When x-axis is in date format, this argument allow to change the format of the tick labels. See strptime for more details.
`major.breaks`	Character. Major x-axis breaks (only when x is in date format). Ex: "weeks", "15days", "months", etc.
`minor.breaks`	Character. Minor x-axis breaks (only when x is in date format). Ex: "weeks", "15days", "months", etc.
`color.palette`	Character. The palette for tip colors. Only palettes from the package `RColorBrewer` are available. See `brewer.pal` documentation for more details.
`legend.position`	Character (or numeric). The position of legends. ("left", "right", "bottom", "top", or two-element numeric vector)

Original versoin by Anton Camacho, modified by Thibaut Jombart.

## load the dataset
data(FluH1N1pdm2009)
attach(FluH1N1pdm2009)

x <- new("obkData", individuals = individuals, dna = FluH1N1pdm2009$dna,
      dna.individualID = samples$individualID, dna.date = samples$date,
      trees = FluH1N1pdm2009$trees)

detach(FluH1N1pdm2009)


## have a look at the summary
summary(x)

## first simple tree
p <- plotggphy(x, ladderize = FALSE)

## build tip attribute and use sample dates to scale the x-axis as date time
p <- plotggphy(x, branch.unit = "year")

## change x breaks and labels
p <- plotggphy(x, branch.unit = "year", major.breaks = "month",
       axis.date.format = "%b%Y")

## color-code tip location
p <- plotggphy(x, branch.unit = "year", show.tip=FALSE, tip.color = "location")

## change tip size and transparency
p <- plotggphy(x, branch.unit = "year", tip.color = "location",
               tip.size = 3, tip.alpha = 0.75)