build_Lifemap: A function to construct a LifemapR object, usable by the...

In damiendevienne/lifemapr: Data Visualisation on 'Lifemap' Tree

A function to construct a LifemapR object, usable by the other functions of the package.

Description

A function to construct a LifemapR object, usable by the other functions of the package.

Usage

build_Lifemap(df, basemap = NULL, verbose = TRUE)

Arguments

df	A dataframe containing at least one column named "taxid" that contains NCBI Taxonomy Identifiers (taxid). The dataframe can contain any number of additional columns defining traits/characters/values associated to each taxid.
basemap	Deprecated argument.
verbose	If TRUE (the default), the function will print detailed information to the console. If FALSE, it will run silently.

Value

A list of class lifemap_obj containing:

• df : a dataframe containing at least for each taxid :

  • The x coordinate (lon)

  • The y coordonate (lat)

  • The scientific name (sci_name)

  • The zoom level at which the taxa is visible (zoom)

  • A list of its ascendants (ascend)

  • Its type ("requested" or "ancestor")

  • Its direct ancestor

  • Its type (type), i.e. whether the taxid was requested by the user ("requested") or if it is the anecestor of a requested taxid ("ancestor")

• basemap : the basemap used to get taxa's details

Examples

data(eukaryotes_80)
## Not run: 
# make sure you have a good internet connection to load these very large files
LM <- build_Lifemap(eukaryotes_80)

## End(Not run)

damiendevienne/lifemapr documentation built on April 12, 2025, 10:47 a.m.