GitHub - lbbe-software/Mondrian: Display the relative occurrence and co-occurrence of events in a sample (original) (raw)
Mondrian: Display the relative occurrence and co-occurrence of events in a sample
The unique function of the Mondrian
package, named mondrian
, allows representing in a single graph the relative occurrence and co-occurrence of events measured in a sample. As examples, the package was applied to describe the occurrence and co-occurrence of different species of bacterial or viral symbionts infecting arthropods at the individual level. The graphics allows determining the prevalence of each symbiont and the patterns of multiple infections (i.e. how different symbionts share or not the same individual hosts). We named the package after the famous painter as the graphical output recalls Mondrian’s paintings.
The package
The stable version of Mondrian
can be installed from CRAN using:
install.packages("Mondrian")
The development version of Mondrian can be installed from GitHub (remotes
needed):
if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("lbbe-software/Mondrian")
Finally load the package in your current R session with the following R command:
The shiny app
A web application (a Shiny
application) is available to use the functionalities of the Mondrian
package in an interactive way. In this application, two examples are shown. The user can also upload its own data and compute the mondrian
function on it. The display output can then be saved.
MondrianShiny
can be run on a R session, doing:
shiny::runApp(system.file("MondrianShiny", package = "Mondrian"))
or online at:https://lbbe-shiny.univ-lyon1.fr/Mondrian/inst/MondrianShiny/
This shiny app is runing with the development version of Mondrian
.
Articles which use Mondrian
functionalities
- _Competitive outcome of multiple infections in a behavior-manipulating virus/wasp interaction._Martinez et al. (2015). Ecology and Evolution, 5(24):5934–5945. doi: 10.1002/ece3.1749
- _Nuclear and cytoplasmic differentiation among Mediterranean populations of Bemisia tabaci: testing the biological relevance of cytotypes._Terraz et al. (2014). Pest Management Science, 70:1503-1513. doi: 10.1002/ps.3792
- _Endosymbiont diversity among sibling weevil species competing for the same resource._Merville et al. (2013). BMC Evolutionary Biology, 13:28. doi: 10.1186/1471-2148-13-28
- _Distribution of Bemisia tabaci (Homoptera: Aleyrodidae) biotypes and their associated symbiotic bacteria on host plants in West Africa._Gnankiné et al. (2013). Insect Conservation and Diversity, 6(3):411-421. doi: 10.1111/j.1752-4598.2012.00206.x
- _Endosymbiont metacommunities, mtDNA diversity and the evolution of the Bemisia tabaci (Hemiptera: Aleyrodidae) species complex._Gueguen et al. (2010). Molecular Ecology, 19(19):4365-76. doi: 10.1111/j.1365-294X.2010.04775.x