pre-assessment {sitePath} | R Documentation |
similarityMatrix
calculates similarity between aligned sequences
The similarity matrix can be used in groupTips
or lineagePath
sneakPeek
is intended to plot similarity as a threshold
against number of output lineagePath. This plot is intended to give user
a feel about how many sitePaths they should expect from
the similarity threshold. The number of lineagePath should not
be too many or too few. The result excludes where the number of lineagePath
is greater than number of tips divided by 20 or self-defined maxPath.
The zero lineagePath result will also be excluded
similarityMatrix(tree) sneakPeek(tree, step = NULL, maxPath = NULL, minPath = 1, makePlot = FALSE)
tree |
The return from |
step |
the similarity window for calculating and ploting. To better see the impact of threshold on path number. This is preferably specified. The default is one 50th of the difference between 1 and minimal pairwise sequence similarity. |
maxPath |
maximum number of path to return show in the plot. The number of path in the raw tree can be far greater than trimmed tree. To better see the impact of threshold on path number. This is preferably specified. The default is one 20th of tree tip number. |
minPath |
minimum number of path to return show in the plot. To better see the impact of threshold on path number. This is preferably specified. The default is 1. |
makePlot |
whether make a dot plot when return |
similarityMatrix
returns a diagonal matrix of
similarity between sequences
sneakPeek
return the similarity threhold against number of lineagePath.
There will be a simple dot plot between threshold and path number if
makePlot
is TRUE.
data("zikv_tree") data("zikv_align") tree <- addMSA(zikv_tree, alignment = zikv_align) simMatrix <- similarityMatrix(tree) sneakPeek(tree)