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, reference = NULL, gapChar = "-", ...) ## S3 method for class 'fixationSites' plotSingleSite(x, site, ...) ## S3 method for class 'multiFixationSites' plotSingleSite(x, site, ...)
x |
A |
site |
One of the mutations in the |
showPath |
If plot the lineage result from lineagePath. |
reference |
Name of reference for site numbering. The name has to be one of the sequences' name. The default uses the intrinsic alignment numbering. |
gapChar |
The character to indicate gap. The numbering will skip the gapChar for the reference sequence. |
... |
Arguments in |
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, 0.996) plotSingleSite(paths, 139) ## Not run: fixations <- fixationSites(paths) plotSingleSite(fixations, 139) ## End(Not run) ## Not run: multiFixations <- multiFixationSites(paths) plotSingleSite(multiFixations, 1542) ## End(Not run)