README.md

In bakuhatsu/measuRoots: For analysis and plotting of root length data output from SmartRoot in imageJ

measuRoots

A package for automated data analysis of wheat root lengths exported from SmartRoot. This package includes the following functions:

mergeCSVs() #merges multiple .csv files exported from SmartRoot into one .csv file (This is also an RStudio addin)
compileRootDF() #processes +0h, +24h, and +48h .csv files & outputs dataframe for plotting
rootPlot() #to plot the data
summaryWSvsWW() #to summarize data for plotting significant differences
plotDifferences() #to plot the differences between WW and WS at each timepoint with significance indicated
rootLengthsApp() #graphical app (and RStudio addin) runs as an RStudio gadget or in web browser 
# The rootLengthsApp utilizes all other functions except mergeCSVs (displays, outputs, return plots & summaries)

Most of the data analysis pipeline can be run from the rootLengthsApp graphical interface. rootLengthsApp is a neat shiny gadget and Rstudio addin that can run in an RStudio window or in a local web browser.

Shiny App in action

Installing and loading the measuRoots package:

Installing through GitHub requires the devtools package, so instructions for installing and loading that package are provided below.

## Install and load devtools for loading packages from GitHub
install.packages("devtools") # to allow us to install packages from GitHub
library(devtools)

Since GitHub packaged are compiled on your machine to run, you may be prompted to "install build tools" or something similar. Follow the instructions, which will install the tools needed to compile this package.

Now you should be ready to install and then load the measuRoots package

install_github("bakuhatsu/measuRoots") # syntax for installing from GitHub: username/library
library(measuRoots) # To load the package (not necessary to directly use the addin version)

Run directly from the command line with:

rootLengthsApp()
# or if the package isn't loaded:
measuRoots::rootLengthsApp()

The app does not require RStudio, but works nicely in this IDE. If run outside of RStudio, will load in the default web browser.

Publication

Nelson, S. K., and Oliver, M. J. (2017). A Soil-Plate Based Pipeline for Assessing Cereal Root Growth in Response to Polyethylene Glycol (PEG)-Induced Water Deficit Stress. Front Plant Sci 8, 1272. doi: 10.3389/fpls.2017.01272

https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2017.01272/full

Example output

bakuhatsu/measuRoots documentation built on March 26, 2024, 8:51 p.m.