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 :
Once installed, load the package with :
Here is a brief introduction on how to use LifemapR.
build_Lifemap
function transform your already existing data into a format usable by LifemapR functionsdata(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 :
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
Go to the package’s folder
then you can simply use the package’s functions