treePlotNew: Plot 'tree' with branch labels colored in a heatmap based on...

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

Plot 'tree' with branch labels colored in a heatmap based on values in 'vals'

Description

Plot 'tree' with branch labels colored in a heatmap based on values in 'vals'

Usage

treePlotNew(
  tree,
  vals = NULL,
  rank = F,
  nlevels = 9,
  type = "c",
  col = NULL,
  maintitle = NULL,
  useedge = F,
  doreroot = F,
  rerootby = NULL,
  useSpecies = NULL,
  species.names = NULL,
  speclist1 = NULL,
  speclist2 = NULL,
  aligntip = F,
  colpan1 = rgb(0, 119, 187, maxColorValue = 255),
  colpan2 = rgb(204, 51, 17, maxColorValue = 255),
  colpanmid = rgb(187, 187, 187, maxColorValue = 255),
  plotspecies = NULL,
  edgetype = NULL,
  textsize = 0.6,
  colbarlab = "",
  splist2sym = "psi",
  dolegend = T,
  nacol = rgb(0, 0, 0),
  figwid = 10,
  ...
)

Arguments

tree.	A phylo object, used for topology
vals.	Values to use for heatmap to color branches, in same order as edges of tree
rank.	Whether to plot ranks instead of values
nlevels.	How many colors to use in the heatmap
type.	Type for plot.phylo
col.	Vector of user-defined colors
maintitle.	Main title label
useedge.	Whether to use edge lengths in 'tree' for plotting
doreroot.	Whether to re-root the tree before plotting
rerootby.	If re-rooting, what to use to root the tree (verify by checking against unrooted plot)
useSpecies.	A vector of species to include in the plot (verify by checking against full set)
species.names.	Data fram for converting names in 'tree' to names to be plotted (row names should be tip labels of tree, and first column should contain the corresponding desired tip labels)
speclist1.	A vector of tip labels to highlight in bold, blue text
speclist2.	A vector of tip labels to which to add an asterisk
aligntip.	Whether to align tip labels (default FALSE)
colpan1.	Color for lowest value in heatmap (default blue)
colpan2.	Color for highest value in heatmap (default rose)
colpanmid.	Color for middle value in heatmap (default gray)
plotspecies.	A vector of tip labels to display on the tree (the remainder will be masked, but the corresponding tips will be plotted on the tree)
edgetype.	Vector of line type for edges.
textsize.	cex value for tip labels (default 0.6)
colbarlab.	Label for the color bar legend
splist2sym.	A value within species names to display as a symbol
dolegend.	Whether to display the heatmap legend.
nacol.	Color to display for any edges with length NA
figwid.	Adjust x limits of plot.phylo by 1/figwid. May be related to figure width (requires some optimization)
....	further arguments to be passed to 'plot' or to 'plot.phylo'

Value

Plots a cladogram of 'tree' with branch colors determined by 'vals'

nclark-lab/RERconverge documentation built on March 2, 2024, 8:51 a.m.