Function to plot phylogenetic tree from the estimated results
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)
)Draw plots of phylogenetic tree.
The estimated results of phylogenetic analysis by `estPhylo` function for one
Name of trait of interest. This will be used in the title of the plots.
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.
If TRUE, the function will return the plot of phylogenetic tree.
The information of subpopulations.
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.
This argument specifies how to save the plot of phylogenetic tree. The function offers `png`, `pdf`, `jpg`, and `tiff`.
A vector of two integers specifying the plot types for the positive and negative genotypic values respectively.
A vector of two integers or chracters specifying color of nodes for the positive and negative genotypic values respectively.
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.
A numeric specifying the maximum point size of the plot.
A numeric specifying the minimum point size of the plot.
If TRUE, the edge branch of phylogenetic tree wiil be colored.
If TRUE, lavels for tips will be shown.
If TRUE, the function will return the ggplot version of phylogenetic tree. It offers the precise information on subgroups for each haplotype.
A numeric specifying the maximum point size of the plot for ggtree, relative to the range of x and y-axes (0 < cexMaxForGG <= 1).
A numeric specifying the minimum point size of the plot for ggtree, relative to the range of x and y-axes (0 < cexMaxForGG <= 1).
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.