Package: LifemapR 1.1.4

Aurélie Siberchicot

LifemapR: Data Visualisation on 'Lifemap' Tree

Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap <http://lifemap.univ-lyon1.fr/>. It takes as input a dataframe with at least a "taxid" column containing NCBI format TaxIds and allows to draw multiple layers with different visualisation tools.

Authors:Cassandra Bompard [aut], Damien M. de Vienne [aut], Aurélie Siberchicot [ctb, cre]

LifemapR_1.1.4.tar.gz
LifemapR_1.1.4.tar.gz(r-4.5-noble)LifemapR_1.1.4.tar.gz(r-4.4-noble)
LifemapR_1.1.4.tgz(r-4.4-emscripten)LifemapR_1.1.4.tgz(r-4.3-emscripten)
LifemapR.pdf |LifemapR.html✨
LifemapR/json (API)

# Install 'LifemapR' in R:

install.packages('LifemapR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lifemap-tol/lifemapr/issues

Datasets:

LM_eukaryotes - Transformation in a LifemapR format of NCBI information for 1000 eukaryotes
eukaryotes_1000 - NCBI information for 1000 eukaryotes
eukaryotes_80 - NCBI information for 80 eukaryotes
gen_res - Genomic results
kraken_res - Kraken results

3.18 score 150 downloads 15 exports 72 dependencies

Last updated 3 months agofrom:5d8c0aec17. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-linux	OK	Oct 30 2024

Exports:build_Lifemap create_matrix display_map draw_Lifemap is.lifemap_obj is.lm_branches is.lm_markers is.lm_piecharts lifemap lm_branches lm_markers lm_piecharts make_newick pass_infos pass_infos_discret

Dependencies:base64enc bitops bslib cachem cli colorspace commonmark cpp11 crayon crosstalk digest dplyr evaluate fansi farver fastmap fastmatch fontawesome fs generics glue highr htmltools htmlwidgets httpuv jquerylib jsonlite knitr labeling later lattice lazyeval leaflet leaflet.minicharts leaflet.providers lifecycle magrittr memoise mime munsell pillar pkgconfig png promises purrr R6 rappdirs raster RColorBrewer Rcpp RCurl rlang rmarkdown sass scales shiny sourcetools sp stringi stringr terra tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun xtable yaml

Use of LifemapR

Cassandra Bompard

Rendered fromrunLifemapR.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-08-01
Started: 2023-08-24

Citation

Readme and manuals

Help Manual

Help page	Topics
Add a graphical element to a tree visualisation.	+.lifemap_obj
Compute the aesthetics for a subtree visualisation.	add_lm_branches
Compute the aesthetics for markers visualisation.	add_lm_markers
Compute the aesthetics for discret values visualisation.	add_lm_piecharts
A function to construct a LifemapR object, usable by the other functions of the package.	build_Lifemap
Create a dataframe for the ancestry.	create_matrix
Compute a new scale for a value	create_value_range
Create a Lifemap base.	display_map
Compute the different display options.	display_option
Represent data on a Lifemap basemap.	draw_Lifemap
NCBI information for 1000 eukaryotes	eukaryotes_1000
NCBI information for 80 eukaryotes	eukaryotes_80
Genomic results	gen_res
Reports whether x is a lifemap_obj object.	is.lifemap_obj
Reports whether x is a lm_branches object.	is.lm_branches
Reports whether x is a lm_markers object.	is.lm_markers
Reports whether x is a lm_branches object.	is.lm_piecharts
Kraken results	kraken_res
Initialise a new Lifemap visualisation.	lifemap
Add a "branches" layer to a lifemap_obj object.	lm_branches
Transformation in a LifemapR format of NCBI information for 1000 eukaryotes	LM_eukaryotes
add a "markers" layer to a lifemap_obj object.	lm_markers
Add a "piecharts" layer to a lifemap_obj object.	lm_piecharts
Create a newick for the given dataset.	make_newick
Infer numerical values to nodes.	pass_infos
Infer discret values to nodes for lm_piecharts function.	pass_infos_discret
Method to print lifemap_obj objects.	print.lifemap_obj