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' (actually the least
percentage of 'major SNP') as a threshold against number of output
lineagePath. This plot is intended to give user a rought view about
how many lineages they could expect from the 'similarity' threshold in
the function lineagePath
. The number of lineagePath is
preferably 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
user-defined maxPath. The zero lineagePath result will also be excluded.
similarityMatrix(tree) sneakPeek(tree, step = 10, 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. The default is 10. |
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. 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)