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CRAN_Release_Badge CRAN Downloads R-CMD-check License: GPL v3 Project Status: Active – The project has reached a stable, usable state and is being actively developed. SWH

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.

  1. 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
  1. 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 :

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

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.
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