plotHaploNetwork: Function to plot haplotype network from the estimated results
In RAINBOWR: Genome-Wide Association Study with SNP-Set Methods

plotHaploNetwork

R Documentation

Function to plot haplotype network from the estimated results

Description

Function to plot haplotype network from the estimated results

Usage

plotHaploNetwork(
  estNetworkRes,
  traitName = NULL,
  blockName = NULL,
  plotNetwork = TRUE,
  subpopInfo = estNetworkRes$subpopInfo,
  saveName = NULL,
  saveStyle = "png",
  plotWhichMDS = 1:2,
  colConnection = c("grey40", "grey60"),
  ltyConnection = c("solid", "dashed"),
  lwdConnection = c(1.5, 0.8),
  pchBase = c(1, 16),
  colCompBase = c(2, 4),
  colHaploBase = c(3, 5, 6),
  cexMax = 2,
  cexMin = 0.7,
  ggPlotNetwork = FALSE,
  cexMaxForGG = 0.025,
  cexMinForGG = 0.008,
  alphaBase = c(0.9, 0.3)
)

Arguments

`estNetworkRes`	The estimated results of haplotype network by 'estNetwork' 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.
`plotNetwork`	If TRUE, the function will return the plot of haplotype network.
`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'.
`plotWhichMDS`	We will show the MDS (multi-dimensional scaling) plot, and this argument is a vector of two integers specifying that will define which MDS dimension will be plotted. The first and second integers correspond to the horizontal and vertical axes, respectively.
`colConnection`	A vector of two integers or characters specifying the colors of connection between nodes for the original and complemented haplotypes, respectively.
`ltyConnection`	A vector of two characters specifying the line types of connection between nodes for the original and complemented haplotypes, respectively.
`lwdConnection`	A vector of two integers specifying the line widths of connection between nodes for the original and complemented haplotypes, respectively.
`pchBase`	A vector of two integers specifying the plot types for the positive and negative genotypic values respectively.
`colCompBase`	A vector of two integers or characters specifying color of complemented haplotypes for the positive and negative genotypic values respectively.
`colHaploBase`	A vector of integers or characters specifying color of original haplotypes 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.
`ggPlotNetwork`	If TRUE, the function will return the ggplot version of haplotype network. It offers the precise information on subgroups for each haplotype.
`cexMaxForGG`	A numeric specifying the maximum point size of the plot for the ggplot version of haplotype network, relative to the range of x and y-axes (0 < cexMaxForGG <= 1).
`cexMinForGG`	A numeric specifying the minimum point size of the plot for the ggplot version of haplotype network, relative to the range of x and y-axes (0 < cexMaxForGG <= 1).
`alphaBase`	alpha (parameter that indicates the opacity of a geom) for original haplotype with positive / negative effects. alpha for complemented haplotype will be same as the alpha for original haplotype with negative effects.