custom_nexus: Color SplitsTree dendrograms

In abrozzi/microbio: R utils for microbiology bioinformatics

Description

Reads a nexus file and adds colors to the leaves

Usage

custom_nexus(
  nexus.file,
  tips,
  colors,
  outfile,
  fromBIGSdb = FALSE,
  fg,
  vlabels,
  w = 20,
  h = 20,
  s = "r",
  f,
  lc,
  lk,
  edgecolor = "gray",
  plot,
  SplitsTree.exe = "/Applications/SplitsTree/SplitsTree"
)

Arguments

tips	(leaves of the dendrogram)
colors	vector of the same length of the tips indicating the color of each tip
vlabels	vector of labels to be plot; leave empty character "" to hide the label.
w	width of the tip. If you indicate a single number it will be recycled. Either provide a vector of widths
h	height of the tip. Same for w.
s	shape of the tip "o" is oval. The other option is "r" rectangle.
f	fonts of the labels. Like "Dialog-BOLD-16" or 'Courier-PLAIN-24'. Other option are: Calibri, Arial, Times. For bold -BOLD and not -PLAIN
lc	vector of label colors
lk	vector of background of the label
edgecolor	the color of the edges
plot	if TRUE SplitsTree is launched and the nexus displayed
Splitstree.exe	path to the executable of SplitsTree

Value

a new nexus file with colors

Examples

inputfile <- file.path(path.package('microbio'),'input.nexus')
outfile <- file.path(path.package('microbio'),'output.nexus')
tips <- c("A","R","G","B")
col <- c("red","blue","green","yellow")
s <- c("r","o","r","o")
ws <- c(10,20,30,40)
hs <- c(10,20,30,40)
fg <- c("blue","orange", "violet", "gray8")
lc <- c("gray", "cyan", "pink", "blue")
lk <- c("black", "blue", "black", "yellow")
edgecolor <- "blue"
f <- c("Arial-BOLD-20", "Calibri-BOLD-16", "Times-20", "Dialog-BOLDITALIC-25")
custom_nexus(nexus.file=inputfile, tips=tips, colors=col, vlabels=tips, w=ws, f=f, h=hs, lc=lc, lk=lk, fg= fg, s=s, edgecolor=edgecolor, outfile=outfile, plot=TRUE, SplitsTree.exe = "/Applications/SplitsTree/SplitsTree")

abrozzi/microbio documentation built on Feb. 8, 2021, 11:34 a.m.