R: Plots for phylogenetic tree and data

plot.phylo4d {adiv}

R Documentation

Plots for phylogenetic tree and data

Description

Functions barp4d, dotp4d and gridp4d provide plots for phylo4d objects (i.e. phylogenetic tree and data). Function plot.phylo4d provides a general interface for all other functions. Function barp4d uses barplots of trait values along the phylogenetic tree. Function dotp4d uses dotplots of trait values along the phylogenetic tree, and function gridp4d gridplots.

Usage

## S3 method for class 'phylo4d'
plot(x, trait = names(tdata(p4d)), center = TRUE, 
    scale = TRUE, plot.type = "barplot", tree.ladderize = FALSE, 
    tree.type = "phylogram", tree.ratio = NULL, 
    tree.xlim = NULL, tree.open.angle = 0, 
    tree.open.crown = TRUE, show.tip = TRUE, tip.labels = NULL, 
    tip.col = "black", tip.cex = 1, tip.font = 3, tip.adj = 0, 
    data.xlim = NULL, bar.lwd = 10, bar.col = "grey35", 
    show.data.axis = TRUE, dot.col = "black", dot.pch = 20, 
    dot.cex = 2, cell.col = topo.colors(100), 
    show.color.scale = TRUE, show.trait = TRUE, 
    trait.labels = NULL, trait.col = "black", 
    trait.cex = 1, trait.font = 1, trait.bg.col = "grey90", 
    error.bar.sup = NULL, error.bar.inf = NULL, 
    error.bar.col = 1, show.box = FALSE, grid.vertical = TRUE,
    grid.horizontal = FALSE, grid.col = "grey25", 
    grid.lty = "dashed", ...) 

barp4d(height, trait = names(tdata(height)), 
    center = TRUE, scale = TRUE, tree.ladderize = FALSE, 
    tree.type = "phylogram", tree.ratio = NULL, 
    tree.xlim = NULL, tree.open.angle = 0, 
    tree.open.crown = TRUE, show.tip = TRUE, tip.labels = NULL, 
    tip.col = "black", tip.cex = 1, tip.font = 3, tip.adj = 0, 
    data.xlim = NULL, bar.lwd = 10, bar.col = "grey35", 
    show.data.axis = TRUE, show.trait = TRUE, 
    trait.labels = NULL, trait.col = "black", trait.cex = 1,
    trait.font = 1, trait.bg.col = "grey90", 
    error.bar.sup = NULL, error.bar.inf = NULL, 
    error.bar.col = 1, show.box = FALSE, grid.vertical = TRUE, 
    grid.horizontal = FALSE, grid.col = "grey25", 
    grid.lty = "dashed", ...) 

dotp4d(p4d, trait = names(tdata(p4d)), center = TRUE, 
    scale = TRUE, tree.ladderize = FALSE, 
    tree.type = "phylogram", tree.ratio = NULL, 
    tree.xlim = NULL, tree.open.angle = 0, 
    tree.open.crown = TRUE, show.tip = TRUE, tip.labels = NULL,
    tip.col = "black", tip.cex = 1, tip.font = 3, 
    tip.adj = 0, data.xlim = NULL, show.data.axis = TRUE, 
    dot.col = "black", dot.pch = 20, dot.cex = 2, 
    show.trait = TRUE, trait.labels = NULL, trait.col = "black", 
    trait.cex = 1, trait.font = 1, trait.bg.col = "grey90", 
    error.bar.sup = NULL, error.bar.inf = NULL, 
    error.bar.col = 1, show.box = FALSE, grid.vertical = FALSE,
    grid.horizontal = TRUE, grid.col = "grey25", 
    grid.lty = "dashed", ...) 

gridp4d(p4d, trait = names(tdata(p4d)), center = TRUE, 
    scale = TRUE, tree.ladderize = FALSE, 
    tree.type = "phylogram", tree.ratio = NULL, 
    tree.xlim = NULL, tree.open.angle = 0, 
    tree.open.crown = TRUE, show.tip = TRUE, tip.labels = NULL, 
    tip.col = "black", tip.cex = 1, tip.font = 3, tip.adj = 0,
    cell.col = topo.colors(100), show.color.scale = TRUE, 
    show.trait = TRUE, trait.labels = NULL, trait.col = "black", 
    trait.cex = 0.7, trait.font = 1, trait.bg.col = "grey90", 
    show.box = FALSE, grid.vertical = FALSE, 
    grid.horizontal = FALSE, grid.col = "grey25", 
    grid.lty = "dashed", ...)

Arguments

`x`, `p4d`, `height`	a `phylo4d` object.
`trait`	the traits in the `phylo4d` object to include in the plot. Can be a character vector giving the name of the traits or numbers giving the column index in the table of the data slot of the `p4d` or `height` object. Can be used to reorder the traits in the plot.
`center`	a logical indicating whether traits values should be centered.
`scale`	a logical indicating whether traits values should be scaled.
`plot.type`	a character string specifying the type of plot for traits data. Can be `"barplot"`, `"dotplot"` or `"gridplot"`.
`tree.ladderize`	a logical indicating whether the tree should be (right) ladderized.
`tree.type`	a character string specifying the type of phylogeny to be drawn. Can be `"phylogram"`, `"cladogram"` or `"fan"`.
`tree.ratio`	a numeric value in [0, 1] giving the proportion of width of the figure for the tree.
`tree.xlim`	a numeric vector of length 2 giving the limits of the x-axis for the tree. If NULL, it is determined automatically.
`tree.open.angle`	a numeric value giving the angle in degrees left blank if `tree.type = "fan"`.
`tree.open.crown`	a logical indicating whether the crowns should be drawn following the value of `tree.open.angle` (default `TRUE`).
`show.tip`	logical indicating whether tips labels should be drawn.
`tip.labels`	character vector to label the tips. If `NULL` the tips labels of the `phylo4d` object are used.
`tip.col`	a vector of R colors to use for the tips labels. Recycled if necessary.
`tip.cex`	a numeric vector to control character size of the tips labels. Recycled if necessary.
`tip.font`	an integer vector specifying the type of font for the tips labels: 1 (plain text), 2 (bold), 3 (italic), or 4 (bold italic). Recycled if necessary.
`tip.adj`	a vector of numeric in [0, 1] to control tips labels justification: 0 (left-justification), 0.5 (centering), or 1 (right-justification). Recycled if necessary.
`data.xlim`	numeric vector of length 2 or matrix giving the x coordinates range for the barplots/dotplots.
`bar.lwd`	a vector of numeric giving bar widths of the barplot(s). Recycled along the tips, reapeated for each trait.
`bar.col`	a vector of R colors to use for the bars. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning.
`show.data.axis`	logical indicating whether barplots/dotplots axes should be drawn.
`dot.col`	a vector of R colors to use for the points. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning.
`dot.pch`	a numerical vector of symbol to use for the points. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning.
`dot.cex`	a numerical vector. Character (or symbol) expansion for the points. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning.
`cell.col`	a vector of colors for `gridplot` cells. Easily generated by `heat.colors`, `topo.colors`, `terrain.colors` or other functions created with `link{colorRampPalette}`.
`show.color.scale`	logical indicating whether color scale should be drawn.
`show.trait`	logical indicating whether traits labels should be drawn.
`trait.labels`	character vector to label the traits. If `NULL` the traits labels of the `phylo4d` object are used.
`trait.col`	a vector of R colors to use for the traits labels. Recycled if necessary.
`trait.cex`	a numeric vector to control character size of the trait labels. Recycled if necessary.
`trait.font`	an integer vector specifying the type of font for the traits labels: 1 (plain text), 2 (bold), 3 (italic), or 4 (bold italic). Recycled if necessary.
`trait.bg.col`	a vector of R colors to use for the background of the barplots. Recycled if necessary.
`error.bar.sup`	a matrix giving the superior limit for error bars. Columns and rows names must match with traits and tips labels, respectively.
`error.bar.inf`	a matrix giving the inferior limit for error bars. Columns and rows names must match with traits and tips labels, respectively.
`error.bar.col`	a vector of R colors to draw error bars.
`show.box`	a logical indicating whether a box should be drawn around the plots.
`grid.vertical`	a logical incating whether vertical lines of the grid should be drawn.
`grid.horizontal`	a logical incating whether horizontal lines of the grid should be drawn.
`grid.col`	a vector of R colors to use for the lines of the grid.
`grid.lty`	the lines type of the grid. Possibly a vector.
`...`	further arguments to be passed to `plot.phylo`.

Author(s)

The four functions were written by Francois Keck in the package named phylosignal. Functions were there named as follows: multiplot.phylo4d, barplot.phylo4d, dotplot.phylo4d, and gridplot.phylo4d. At the end of 2019, the package was orphaned and the functions were integrated in package adiv. The versions of the functions have been slightly modified compared to those developed by Francois Keck.

Examples

if(require(ape) && require(phylobase)){
data(batcomm)
# Phylogenetic tree for bat species
phy <- read.tree(text = batcomm$tre)
# Abondance data plotted in front of the phylogeny
# F = rainforest, P = cacao plantation
# O = oldfields, C = cornfields
ab.4d <- phylo4d(phy, t(batcomm$ab))
barp4d(ab.4d, center = FALSE, scale = FALSE, 
    data.xlim = c(0, max(batcomm$ab)))
dotp4d(ab.4d, center = FALSE, scale = FALSE, 
    data.xlim = c(0, max(batcomm$ab)))
gridp4d(ab.4d, center = FALSE, scale = FALSE)
}

[Package adiv version 2.2.1 Index]