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

Source: R/build_Lifemap.R
build_Lifemap.Rd

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

Usage

build_Lifemap(df, basemap = c("ncbi", "base", "fr", "virus"), 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

The chosen basemap for Lifemap ("fr", "ncbi", "base" or "virus").

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)
if (FALSE) { # \dontrun{
# make sure you have a good internet connection to load these very large files
LM <- build_Lifemap(eukaryotes_80, "fr")
} # }