Visualize the results

The plot function to visualize the return of functions in the package. The underlying function applies ggplot2. The function name plot is used to keep the compatibility with previous versions, but they do not behave like the generic plot function since 1.5.4.

A phyMSAmatched object will be plotted as a tree diagram.

A lineagePath object will be plotted as a tree diagram and paths are black solid line while the trimmed nodes and tips will use gray dashed line.

A parallelSites object will be plotted as original phylogenetic tree marked with parallel mutations attached as dot plot.

A fixationSites object will be plotted as original phylogenetic tree marked with fixation substitutions.

A sitePath object can be extracted by using extractSite on the return of fixationSites.

A fixationIndels object will be plotted as original phylogenetic tree marked with indel fixation.

A fixationPath object will be plotted as a phylo object. The tips are clustered according to the fixation sites. The transition of fixation sites will be plotted as a phylogenetic tree. The length of each branch represents the number of fixation mutation between two clusters.

# S3 method for phyMSAmatched
plot(x, y = TRUE, ...)

# S3 method for lineagePath
plot(x, y = TRUE, showTips = FALSE, ...)

# S3 method for parallelSites
plot(x, y = TRUE, ...)

# S3 method for fixationSites
plot(x, y = TRUE, tipsGrouping = NULL, ...)

# S3 method for sitePath
plot(x, y = NULL, select = NULL, showTips = FALSE, ...)

# S3 method for fixationIndels
plot(x, y = TRUE, ...)

# S3 method for fixationPath
plot(x, y = TRUE, ...)

Arguments

x

The object to plot.

y

Whether to show the fixation mutation between clusters. For lineagePath object and sitePath object, it is deprecated and no longer have effect since 1.5.4.

...

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.

showTips

Whether to plot the tip labels. The default is FALSE.

tipsGrouping

A list to hold the grouping of tips for how the tree will be colored.

select

For a sitePath object, it can have result on more than one evolution pathway. This is to select which path to plot. The default is NULL which will plot all the paths. It is the same as select in plotSingleSite.

Value

A ggplot object to make the plot.

Examples

data(zikv_tree)
data(zikv_align)
tree <- addMSA(zikv_tree, alignment = zikv_align)
plot(tree)

paths <- lineagePath(tree)
plot(paths)

parallel <- parallelSites(paths)
plot(parallel)

fixations <- fixationSites(paths)
plot(fixations)

sp <- extractSite(fixations, 139)
plot(sp)

x <- fixationPath(fixations)
plot(x)