plot.dendromap: Plot dendromap object

In reptalex/dendromap: dendromap: R package for using time-scaled reference trees to scale microbial phylogenies.

Description

Plot dendromap object

Usage

## S3 method for class 'dendromap'
plot(
  x,
  y = NULL,
  color.fcn.clade = viridis::viridis,
  color.fcn.node = viridis::viridis,
  heatmap.offset = 0,
  col.tr.left = 0.5,
  col.tr.width = 0.45,
  col.tr.bottom = 0.75,
  col.point.size = 3,
  row.point.size = 3,
  highlight_basal = TRUE
)

Arguments

x	dendromap class object from treeSim or dendromap
y	optional data matrix. Must have labelled rows containing all tips in x$row.tree and likewise for x$col.tree
color.fcn.clade	color function for clade highlights in ggtree
color.fcn.node	color function for node circles
heatmap.offset	offset put into gheatmap. Defualt is 0
col.tr.left	Left side boundary of column tree. Default is 0.5
col.tr.width	Width of column tree. Default is 0.45
col.tr.bottom	Bottom of column tree. Deafult is 0.75

Examples

set.seed(3)
m=1e3
n=7
row.tree <- rtree(m) %>% phytools::force.ultrametric()
col.tree <- rtree(n)

S <- treeSim(10,row.tree,col.tree,prob.row=0.7,prob.col=0.8,
             col.node = n+1,fix.col.node = T,sd = 1e3,
             row.depth.min=2,row.depth.max=3)

plot(S,col.tr.left = 0.47,
     col.tr.width = 0.505,
     col.tr.bottom = 0.74)

reptalex/dendromap documentation built on April 19, 2021, 5:13 a.m.