plotPhyloTree {RAINBOWR}

Function to plot phylogenetic tree from the estimated results

Description

Function to plot phylogenetic tree from the estimated results

Usage

plotPhyloTree(
  estPhyloRes,
  traitName = NULL,
  blockName = NULL,
  plotTree = TRUE,
  subpopInfo = estPhyloRes$subpopInfo,
  saveName = NULL,
  saveStyle = "png",
  pchBase = c(1, 16),
  colNodeBase = c(2, 4),
  colTipBase = c(3, 5, 6),
  cexMax = 2,
  cexMin = 0.7,
  edgeColoring = TRUE,
  tipLabel = TRUE,
  ggPlotTree = FALSE,
  cexMaxForGG = 0.12,
  cexMinForGG = 0.06,
  alphaBase = c(0.9, 0.3)
)

Arguments

estPhyloRes

The estimated results of phylogenetic analysis by 'estPhylo' function for one

traitName

Name of trait of interest. This will be used in the title of the plots.

blockName

You can specify the haplotype block (or gene set, SNP-set) of interest by the name of haplotype block in 'geno'. This will be used in the title of the plots.

plotTree

If TRUE, the function will return the plot of phylogenetic tree.

subpopInfo

The information of subpopulations.

saveName

When drawing any plot, you can save plots in png format. In saveName, you should substitute the name you want to save. When saveName = NULL, the plot is not saved.

saveStyle

This argument specifies how to save the plot of phylogenetic tree. The function offers 'png', 'pdf', 'jpg', and 'tiff'.

pchBase

A vector of two integers specifying the plot types for the positive and negative genotypic values respectively.

colNodeBase

A vector of two integers or chracters specifying color of nodes for the positive and negative genotypic values respectively.

colTipBase

A vector of integers or chracters specifying color of tips for the positive and negative genotypic values respectively. The length of the vector should equal to the number of subpopulations.

cexMax

A numeric specifying the maximum point size of the plot.

cexMin

A numeric specifying the minimum point size of the plot.

edgeColoring

If TRUE, the edge branch of phylogenetic tree wiil be colored.

tipLabel

If TRUE, lavels for tips will be shown.

ggPlotTree

If TRUE, the function will return the ggplot version of phylogenetic tree. It offers the precise information on subgroups for each haplotype.

cexMaxForGG

A numeric specifying the maximum point size of the plot for ggtree, relative to the range of x and y-axes (0 < cexMaxForGG <= 1).

cexMinForGG

A numeric specifying the minimum point size of the plot for ggtree, relative to the range of x and y-axes (0 < cexMaxForGG <= 1).

alphaBase

alpha (parameter that indicates the opacity of a geom) for tip with positive / negative effects. alpha for node will be same as the alpha for tip with negative effects.

Value

Draw plots of phylogenetic tree.