plotHaploNetwork {RAINBOWR}

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.

Value

Draw plot of haplotype network.