RRphylo (version 2.8.0)

retrieve.angles: Extracting a user-specified subset of the evo.dir results

Description

This function takes the result list produced by evo.dir as the input, and extracts a specific subset of it. The user may specify whether to extract the set of angles between species resultant vectors and the MRCA, the size of resultant vectors, or the set of angles between species.

Usage

retrieve.angles(angles.res,wishlist=c("anglesMRCA","angleDir","angles.between.species"),
  random=c("yes","no"),focus=c("node","species","both","none"),
 node=NULL,species=NULL,write2csv=c("no","yes"),csvfile=NULL)

Value

retrieve.angles outputs an object of class 'data.frame'.

If wishlist = "anglesMRCA", the data frame includes:

• species species ID

• angle the angle between the resultant vector of species and the MRCA

• vector.size the size of the resultant vector computed from species to MRCA

If wishlist = "angleDir", the data frame includes:

• species species ID

• angle.direction the angle between the vector of species and a fixed reference

• vector.size the size of the vector of species

If wishlist = "angles.between.species", the data frame includes:

• species pair IDs of the species pair the "angle between species" is computed for

• angleBTWspecies2MRCA angle between species resultant vectors to MRCA

• anglesBTWspecies angle between species resultant vectors

Arguments

angles.res

the object resulting from evo.dir function.

wishlist

specifies whether to extract angles and sizes ("anglesMRCA") of resultant vectors between individual species and the MRCA, angles and sizes ("angleDir") of vectors between individual species and a fixed reference vector (the same for all species), or angles between species resultant vectors ("angles.between.species").

random

it needs to be "yes" if 'angles.res' object contains randomization results.

focus

it can be "node", "species", "both", or "none", whether the user wants the results for a focal node, or for a given species, for both, or just wants to visualize everything.

node

must be indicated if focus = "node" or "both". As for evo.dir, the node number must refer to the dichotomic version of the original tree, as produced by RRphylo.

species

must be indicated if focus = "species" or "both".

write2csv

has been deprecated; please see the argument csvfile instead.

csvfile

if results should be saved to a .csv file, a character indicating the name of the csv file and the path where it is to be saved. If no path is indicated the file is stored in the working directory. If left unspecified, no file will be saved.

Author

Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto

Details

retrieve.angles allows to focalize the extraction to a particular node, species, or both. Otherwise it returns the whole dataset.

Examples

if (FALSE) {
    data("DataApes")
    DataApes$PCstage->PCstage
    DataApes$Tstage->Tstage

    cc<- 2/parallel::detectCores()
    RRphylo(tree=Tstage,y=PCstage,clus=cc)->RR

# Case 1. "evo.dir" without performing randomization
    evo.dir(RR,angle.dimension="rates",pair.type="node",
    node=  57,random="no")->evo.p

 # Case 1.1 angles and sizes of resultant vectors between individual species and the MRCA:
  # for a focal node
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="node",
    node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="species",
    species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="both",
    node=68,species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="no",focus="none")

 # Case 1.2 angles and sizes of vectors between individual species
 #and a fixed reference vector:
  # for a focal node
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="node",
    node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="species",
    species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="both",
    node=68,species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angleDir",random="no",focus="none")

 # Case 1.3 angles between species resultant vectors:
  # for a focal node
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="node", node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="species", species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="both",node=68,species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angles.between.species",random="no",
    focus="none")


# Case 2. "evo.dir" with performing randomization
    evo.dir(RR,angle.dimension="rates",pair.type="node",node=57,
    random="yes",nrep=10)->evo.p

 # Case 2.1 angles and sizes of resultant vectors between individual species and the MRCA:
  # for a focal node
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes",focus="node",
    node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes", focus="species",
    species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes",focus="both",
    node=68,species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="anglesMRCA",random="yes",focus="none")

 # Case 2.2 angles and sizes of vectors between individual species and a fixed reference vector:
  # for a focal node
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="node",
    node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="species",
    species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="both",
    node=68, species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angleDir",random="yes",focus="none")

 # Case 2.3 retrieve angles between species resultant vectors:
  # for a focal node
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="node", node=68)
  # for a focal species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="species", species="Sap")
  # for both focal node and species
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="both",node=68,species="Sap")
  # without any specific requirement
    retrieve.angles(evo.p,wishlist="angles.between.species",random="yes",
    focus="none")
    }