plotPhyloTree: Function to plot phylogenetic tree from the estimated results
In RAINBOWR: Genome-Wide Association Study with SNP-Set Methods

plotPhyloTree

R Documentation

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.