Data Visualisation on 'Lifemap' Tree.
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 and the name of the basemap chosen. These elements are accessible as following :
full_df <- LM_obj$df
basemap <- LM_obj$basemap
- Then you can display a map with wanted informations by calling one ore more
LifemapR
functions. Note that with theLifemapR
functions, ashiny
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
[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
require(devtools)
devtools::load_all()
then you can simply use the package's functions.