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LifemapR

An R package to visualise data on a Lifemap base (https://lifemap-ncbi.univ-lyon1.fr/)

Installation

To install the development version of LifemapR from GitHub :

remotes::install_github("damiendevienne/LifemapR")

Once installed, load the package with :

require("LifemapR")

Usage

Here is a brief introduction on how to use LifemapR.

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

data(eukaryotes_1000)

# Construction of a LifemapR usable dataframe
LM_obj <- LifemapR::build_Lifemap(eukaryotes_1000)

After the build_Lifemap function the result is a LifemapR format containing a dataframe and the name of the basemap chosen. These elements are accessible as following :

full_df <- LM_obj$df
basemap <- LM_obj$basemap

2. 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

# Initialise a visualisation for LM_obj
lifemap(LM_obj) + 
    # adding a subtree with colored branches
    LifemapR::lm_branches(var_col = "Protein", FUN = mean, col = "PiYG")+
    # adding a set of points
    LifemapR::lm_markers(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

• Redo pass_info function to only infer unknown values and only from the value of direct ancestors
• Implement popups and labels for markers
• Implement popups and labels for polylines
• Black background on leaflet
• Repair the size legend
• Option to thicker the line depending on a variable
• Improve create_matrix function to pass check

How to use during development

Go to the package’s folder

require(devtools)
devtools::load_all()

then you can simply use the package’s functions

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.