lifemapr

https://github.com/lifemap-tol/lifemapr

Science Score: 26.0%

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CITATION.cff file
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codemeta.json file
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.zenodo.json file
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Low similarity (14.1%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: Lifemap-ToL
License: other
Language: R
Default Branch: main
Homepage: https://Lifemap-ToL.github.io/LifemapR/
Size: 16.6 MB

Statistics

Stars: 7
Watchers: 3
Forks: 1
Open Issues: 0
Releases: 5

Created over 3 years ago · Last pushed 10 months ago

Metadata Files

Readme License Codemeta

LifemapR

An R package to visualise data on a Lifemap base (https://lifemap.cnrs.fr/)

Installation

To install the development version of LifemapR from GitHub :

r remotes::install_github("damiendevienne/LifemapR")

Once installed, load the package with :

r require("LifemapR")

Usage

Here is a brief introduction on how to use LifemapR.

With the build_Lifemap function transform your already existing data into a format usable by LifemapR functions

```r data(eukaryotes_1000)

Construction of a LifemapR usable dataframe

LMobj <- LifemapR::buildLifemap(eukaryotes_1000) ```

After the build_Lifemap function the result is a LifemapR format containing a dataframe :

r full_df <- LM_obj$df

Then you can display a map with wanted informations by calling one ore more LifemapR functions. Note that with the LifemapR functions, a shiny application will be launched

```r

Initialise a visualisation for LM_obj

lifemap(LMobj) + # adding a subtree with colored branches LifemapR::lmbranches(varcol = "Protein", FUN = mean, col = "PiYG")+ # adding a set of points LifemapR::lmmarkers(radius = "GC.", var_fillColor = "Genes", FUN = mean) ```

Development

To do list :

[ ] New protocole to fetch data with improved databases (parquet format)
[ ] Improve create_matrix() to use less CPU (merge before joining all lists)
[ ] Improve make_newick() to make it recursive
[ ] Improve the shiny application version
[x] Redo pass_info function to only infer unknown values and only from the value of direct ancestors
[x] Implement popups and labels for markers
[ ] Implement popups and labels for polylines
[x] Black background on leaflet
[x] Repair the size legend
[x] Option to thicker the line depending on a variable
[x] Improve create_matrix function to pass check

How to use during development

Go to the package's folder

r require(devtools) devtools::load_all()

then you can simply use the package's functions

Owner

Name: Lifemap-ToL
Login: Lifemap-ToL
Kind: organization

Repositories: 1
Profile: https://github.com/Lifemap-ToL

CodeMeta (codemeta.json)

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  "description": "Allow to visualise data on the NCBI phylogenetic tree as presented in Lifemap <https://lifemap.cnrs.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.",
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GitHub Events

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Pull request event: 3
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r-lib/actions/check-r-package v2 composite
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r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action 4.1.4 composite
actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

DESCRIPTION cran

R >= 3.5.0 depends
dplyr * imports
htmltools * imports
jsonlite * imports
leaflet * imports
leaflet.minicharts * imports
rlang * imports
shiny * imports
knitr * suggests

.github/workflows/R-CMD-build.yaml actions

actions/checkout v4 composite
actions/upload-artifact v4 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

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