Marklifemap is a tool to visualizing your own data on a lifemap.

Marklifemap allows you to visualize your own dataset on a lifemap version that you can choose, accessible from http://lifemap.univ-lyon1.fr/.

Marklifemap is written in R language.

Installation

Marklifemap is not yet on CRAN. To install the development version:

1. Install the release version of devtools from CRAN with install.packages("devtools").
2. Launch R and type:

library(devtools)
install_github("cassandreheritier/marklifemap")

3. Once installed the package can be loaded using:

library("marklifemap")

Usage

1. Create your dataframe of dataset, with a first vector of taxids and vectors after of datasets to visualize.

data<-data.frame(yourdataset)

2. Run marklifemap with your dataset (possible options are described below).

marklifemap(data, map='ncbi', minimap=TRUE)

Options

The marklifemap() function is called as follows by default:

marklifemap(data, map='standard', minimap=FALSE, ascendant=FALSE, descendant=FALSE, popup="none", form="none", cluster="none")

Possible options are:
map: You can choose the map among 'standard', 'ncbi', 'virus' and 'french' version.
minimap: If minimap is TRUE, another map is opened in the window, to view where you are in the tree.
ascendant: If ascendant is TRUE, all of ascendants of the taxids are shown on the lifemap.
descendant: If descendant is TRUE, all of descendants of the taxids are shown on the lifemap.
popup: You can choose the type of popup you want to view among 'dataframe' (your data are directly shown), 'sci_info' (to view informations from the Solr database about your taxids) and 'none'.
form: You can choose the form of markers among 'dataframe' (markers will be proportionals to your data numbers), 'nbdesc' (with informations from Solr) and 'none'.
cluster: You can choose the type of cluster among 'sum' and 'none'.
output: You can choose to display the search result of the request from Solr, taping 'file' to create a file in your working directory, 'merge_file' to do the same but adding your dataset, 'console' to display in the console directly and 'merge_console' with your dataset again.
filename: If 'file' in 'output' option was given, you can choose the filename.

3. See your lifemap with markers A window appears with your lifemap, enjoy !

Initialization

To understand the functions under marklifemap with a dataset.

### create a set of data in data.frame
# first vector : example of taxids to target, Primates, Bacteria and Anaeroplasma abactoclasticum
# second vector : example of popups that you want to visualize on each taxon (with order)
# third vector : example of number of descendants you want to impose by taxon
# on a NCBI lifemap version
data<-data.frame(list("taxid"=c(2,9443,2087),"name"=c('FIRST','SECOND','THIRD'),"nbdesc"=c(300,20,109)))

### functions called
# get taxids in a vector
taxids=c(2,9443,2087)
solr_request(taxids) # function that calls database Solr, you can find names, coordinates and number of descendants of each taxon
newmap() # create a standard map
newmap(map='virus') # with virusmap

## principal function
marklifemap(data, map='ncbi', popup='dataframe', form='dataframe') # an example of lifemap with markers

Example

# with options 'cluster' and 'output'
marklifemap(data, map='ncbi', popup='dataframe', form='dataframe', cluster='sum', output='file') # with a set of data initialized as before
marklifemap(data, map='ncbi', popup='sci_info', form='nbdesc', minimap=TRUE) # with a minimap and popup informations from Solr

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References

Damien DE VIENNE Package 'leaflet'

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For comments, suggestions and bug reports, please open an issue on this github repository.