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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
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.