Similar protocols

Protocol publication

[…] archiDART is an R package developed for the automated analysis of plant root system architectures using Data Analysis of Root Tracings (DART) and Root System Markup Language files (RSML) . The version 3.0 of archiDART can be downloaded from the CRAN repository. An overview of the functions available in the package is presented in . Among the 10 functions developed for the package, 5 were already presented elsewhere and will not be further discussed in this paper.In comparison with the version presented earlier, the version 3.0 of the package supports the analysis of 3D root systems. In addition, time series data in RSML files can be analysed if the root system age is stored as a continuous function along the root segments. Finally, we developed a set of 5 new functions and updated the architect function to allow the topological analysis of plant root systems. The architect function is now able to calculate the topological indices introduced by Fitter , and the 5 new functions presented in this paper are devoted to the topological analysis of root systems using persistent homology . [...] In order to demonstrate and illustrate the capabilities of archiDART, we developed a web application (archiShiny) using the Shiny library . This application is freely available here: https://plantmodelling.shinyapps.io/archidart. We developed archiShiny with the following aims in mind: (1) demonstrating how multivariate statistical tools (such as principal component analysis) can be used on the aggregated metrics computed by the architect function to differentiate root systems; (2) showing how root systems can be plotted using the advanced graphical functions of the ggplot2 library ; and (3) comparing the topology of root systems using persistent homology. The web application uses a library of 70 RSML files created using the root architecture model ArchiSimple . Based on the initial values of the parameters of the model, the root systems were classified into seven genotypes (mock, dense, sparse, steep, shallow, slow, and fast). Each genotype was represented by 10 simulations. The different genotypes were based on a standard parameter set (mock) and had one parameter changed: growth rate (slow vs. fast), inter-lateral distance (dense vs sparse) or gravitropism (steep vs shallow). […]

Pipeline specifications