README.md
In LifemapR: Data Visualisation on 'Lifemap' Tree

LifemapR

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

To install the development version of LifemapR from GitHub :

remotes::install_github("damiendevienne/LifemapR")

Once installed, load the package with :

require("LifemapR")

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)

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