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
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LifemapR_1.1.4.tgz(r-4.4-any)LifemapR_1.1.4.tgz(r-4.3-any)
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LifemapR.pdf |LifemapR.html✨
LifemapR/json (API)

# Install 'LifemapR' in R:
install.packages('LifemapR', repos = c('https://lifemap-tol.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Datasets:

On CRAN:

5.87 score 7 stars 185 downloads 15 exports 72 dependencies

Last updated 4 months agofrom:eaf6cfe1df. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winOKNov 12 2024
R-4.5-linuxOKNov 12 2024
R-4.4-winOKNov 12 2024
R-4.4-macOKNov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:build_Lifemapcreate_matrixdisplay_mapdraw_Lifemapis.lifemap_objis.lm_branchesis.lm_markersis.lm_piechartslifemaplm_brancheslm_markerslm_piechartsmake_newickpass_infospass_infos_discret

Dependencies:base64encbitopsbslibcachemclicolorspacecommonmarkcpp11crayoncrosstalkdigestdplyrevaluatefansifarverfastmapfastmatchfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetshttpuvjquerylibjsonliteknitrlabelinglaterlatticelazyevalleafletleaflet.minichartsleaflet.providerslifecyclemagrittrmemoisemimemunsellpillarpkgconfigpngpromisespurrrR6rappdirsrasterRColorBrewerRcppRCurlrlangrmarkdownsassscalesshinysourcetoolsspstringistringrterratibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableyaml

Use of LifemapR

Cassandra Bompard

Rendered fromrunLifemapR.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2024-07-31
Started: 2023-07-04

Readme and manuals

Help Manual

Help pageTopics
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 valuecreate_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 eukaryoteseukaryotes_1000
NCBI information for 80 eukaryoteseukaryotes_80
Genomic resultsgen_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 resultskraken_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 eukaryotesLM_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