Uses the original distance matrix created by
distanceMatrix and the least cost path matrix created by
leastCostMatrix to find the least cost path between the first and the last cells of the matrix. If
leastCostMatrix, then it must be
TRUE when using this function. Otherwise, the default is
FALSE in both.
leastCostPath( distance.matrix = NULL, least.cost.matrix = NULL, diagonal = FALSE, parallel.execution = TRUE )
numeric matrix or list of numeric matrices, a distance matrix produced by
numeric matrix or list of numeric matrices produced by
Alist of dataframes if
least.cost.matrix is a list, or a dataframe if
least.cost.matrix is a matrix. The dataframe/s have the following columns:
A row/sample of one of the sequences.
B row/sample of one the other sequence.
distance distance between both samples, extracted from
cumulative.distance cumulative distance at the samples
#loading data data(sequenceA) data(sequenceB) #preparing datasets AB.sequences <- prepareSequences( sequence.A = sequenceA, sequence.A.name = "A", sequence.B = sequenceB, sequence.B.name = "B", merge.mode = "complete", if.empty.cases = "zero", transformation = "hellinger" ) #computing distance matrix AB.distance.matrix <- distanceMatrix( sequences = AB.sequences, grouping.column = "id", method = "manhattan", parallel.execution = FALSE ) #computing least cost matrix AB.least.cost.matrix <- leastCostMatrix( distance.matrix = AB.distance.matrix, diagonal = FALSE, parallel.execution = FALSE ) AB.least.cost.path <- leastCostPath( distance.matrix = AB.distance.matrix, least.cost.matrix = AB.least.cost.matrix, parallel.execution = FALSE ) #plot plotMatrix(distance.matrix = AB.distance.matrix, least.cost.path = AB.least.cost.path, )