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.

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 :

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

# 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