Description Usage Arguments Value Examples
Plots the output matrices of distanceMatrix
and leastCostMatrix
, and superimposes the least cost path generated by leastCostPath
. This functions relies on image.plot
to plot a color scale along with the matrix plot, or image
when a color scale is not needed.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 
distance.matrix 
numeric matrix or list of numeric matrices either produced by 
least.cost.path 
dataframe or list of fdataframes produced by 
plot.columns 
number of columns of the output plot if the inputs are lists. If not provided, it is computed automatically by 
plot.rows 
number of rows of the output plot if the inputs are lists. If not provided, it is computed automatically by 
legend 
boolean. If 
color.palette 
string defining the color palette to be used, or a color palette. Accepted strings are "divergent" (default), which uses a redwhiteblue divergent palette produced by the code 
path.color 
string, color of the line representing the least cost path if 
path.width 
line width (lwd) of the plotted path. 
margins 
a numeric vector with four positions indicating the margins of each plotted matrix. Order of margins in this vector is: bottom, left, top, right. 
pdf.filename 
character string with the name, without extension, of the pdf to be written. If 
pdf.width 
with in inches of the output pdf. Default value is 7. 
pdf.height 
height in inches of the output pdf. Default value is 4. 
pdf.pointsize 
base font size of the output pdf. 
rotate 
boolean, if 
A list 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 distance.matrix
.
cumulative.distance cumulative distance at the samples A
and B
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33  #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
)
#plot
plotMatrix(distance.matrix = AB.distance.matrix)
#viridis palette
plotMatrix(distance.matrix = AB.distance.matrix,
color.palette = "viridis")
#custom palette
plotMatrix(distance.matrix = AB.distance.matrix,
color.palette = viridis::viridis(8, option = "B", direction = 1))

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