Package index • LifemapR

All functions

LM_eukaryotes: Transformation in a LifemapR format of NCBI information for 1000 eukaryotes

add_lm_branches(): Compute the aesthetics for a subtree visualisation.

add_lm_markers(): Compute the aesthetics for markers visualisation.

add_lm_piecharts(): Compute the aesthetics for discret values visualisation.

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

create_matrix(): Create a dataframe for the ancestry.

create_value_range(): Compute a new scale for a value

display_map(): Create a Lifemap base.

display_option(): Compute the different display options.

draw_Lifemap(): Represent data on a Lifemap basemap.

eukaryotes_1000: NCBI information for 1000 eukaryotes

eukaryotes_80: NCBI information for 80 eukaryotes

gen_res: Genomic results

is.lifemap_obj(): Reports whether x is a lifemap_obj object.

is.lm_branches(): Reports whether x is a lm_branches object.

is.lm_markers(): Reports whether x is a lm_markers object.

is.lm_piecharts(): Reports whether x is a lm_branches object.

kraken_res: Kraken results

lifemap(): Initialise a new Lifemap visualisation.

lm_branches(): Add a "branches" layer to a lifemap_obj object.

lm_markers(): add a "markers" layer to a lifemap_obj object.

lm_piecharts(): Add a "piecharts" layer to a lifemap_obj object.

make_newick(): Create a newick for the given dataset.

pass_infos(): Infer numerical values to nodes.

pass_infos_discret(): Infer discret values to nodes for lm_piecharts function.

`+`(<lifemap_obj>): Add a graphical element to a tree visualisation.

print(<lifemap_obj>): Method to print lifemap_obj objects.