`plotMatrix.Rd`

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.

plotMatrix( distance.matrix = NULL, least.cost.path = NULL, plot.columns = NULL, plot.rows = NULL, legend = TRUE, color.palette = "divergent", path.color = "black", path.width = 1, margins = c(2,3,2,4), pdf.filename = NULL, pdf.width = 7, pdf.height = 4, pdf.pointsize = 12, rotate = FALSE )

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 red-white-blue 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`

.

#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))