Plot and color the tree according to amino acid/nucleotide of
the selected site. The color scheme depends on the
seqType set in
lineagePath, the tree will be colored
according to the amino acid of the site. The color scheme tries to assign
distinguishable color for each amino acid.
parallelSites, the tree will be colored
according to the amino acid of the site if the mutation is not fixed.
fixationSites, it will color the ancestral
tips in red, descendant tips in blue and excluded tips in grey.
plotSingleSite(x, site, ...) # S3 method for lineagePath plotSingleSite(x, site, showPath = TRUE, showTips = FALSE, ...) # S3 method for sitesMinEntropy plotSingleSite(x, site, ...) # S3 method for parallelSites plotSingleSite(x, site, showPath = TRUE, ...) # S3 method for fixationSites plotSingleSite(x, site, select = NULL, ...)
The object to plot.
lineagePath, it can be any site within sequence
parallelSites, it is restrained
to a predicted fixation site. The numbering is consistent with the
reference defined by
Other arguments. Since 1.5.4, the function uses
ggtree as the base function to make plots so the arguments in
plot.phylo will no longer work.
If plot the lineage result from
The default is
Whether to plot the tip labels. The default is
Select which fixation path in to plot. The default is NULL which will plot all the fixations.
Since 1.5.4, the function returns a ggplot object so on longer
behaviors like the generic