OutbreakTools (version 0.1-0)

plotggphy: Function to plot phylogenies using ggplot2

Description

Function to plot phylogenies using ggplot2

Usage

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")

Arguments

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

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

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)

Examples

## 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)