plotSingleSite {sitePath} | R Documentation |
For 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.
For fixationSites
, it will color the ancestral tips in red,
descendant tips in blue and excluded tips in grey.
For multiFixationSites
, it will color the tips which have
their site fixed. The color will use the same amino acid color
scheme as plotSingleSite.lineagePath
## S3 method for class 'lineagePath' plotSingleSite(x, site, showPath = FALSE, showTips = FALSE, ...) ## S3 method for class 'fixationSites' plotSingleSite(x, site, select = NULL, ...) ## S3 method for class 'multiFixationSites' plotSingleSite(x, site, select = NULL, ...)
x |
A |
site |
One of the mutations in the |
showPath |
If plot the lineage result from lineagePath. |
showTips |
Whether to plot the tip labels. The default is |
... |
Arguments in |
select |
Select which fixation path in to plot. The default is NULL which will plot all the fixations. |
The function only makes plot and returns no value
(It behaviors like the generic plot
function).
data(zikv_tree) data(zikv_align) tree <- addMSA(zikv_tree, alignment = zikv_align) paths <- lineagePath(tree) plotSingleSite(paths, 139) fixations <- fixationSites(paths) plotSingleSite(fixations, 139) ## Not run: multiFixations <- multiFixationSites(paths) plotSingleSite(multiFixations, 1542) ## End(Not run)