/* * This file is part of PaCeQuant. * * Copyright (C) 2017 * * PaCeQuant is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * PaCeQuant is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . * * Fore more information on PaCeQuant and MiToBo, visit * * http://www.informatik.uni-halle.de/mitobo/ * */ ####################################################################################################### # README for evaluating PaCeQuant (PaCeQuantEval) output # # # # Please cite our publication # # B. Möller, Y. Poeschl, R. Plötner, and K. Bürstenbinder. Pacequant: A tool for high-throughput # # quantification of pavement cell shape characteristics. Plant Physiology, 2017. # # when you use PaCeQuantEval. # # # # corresponding PaCeQuantEval author: Yvonne Poeschl (yvonne.poeschl@idiv.de) # # # # Date: 2017/09/25 # ####################################################################################################### Dear user, for visual inspection of PaCeQuant results we provide the R script 'PaCeQuantEval.R' and additional helper scripts (functions.r and functions_plots.r) and a feature mapping contained in the meta folder. For visualizing results follow the instructions below: 1. Make sure that you have installed R or RStudio. 2. Make sure that have installed the following five packages: caroline, gplots, dunn.test, RColorBrewer -> provided by CRAN (www.r-project.org or http://ftp5.gwdg.de/pub/misc/cran/) and multtest -> provided by Bioconductor (http://bioconductor.org/packages/devel/BiocViews.html#___Software) 3. Open the script file 'PaCeQuantEval.R' either in a text editor of your choice or directly in RStudio. Set the variables in the header of the file to the appropriate values, in particular the folders where the PaCeQuant result data are located and the output directory for the final plots have to be specified. You can redefine plot labels and plot colors in the file 'data_description.csv' which is created in the step 'Setting up environment' in the 'PaCeQuantEval.R' script. 4. Run the script. In RStudio you can simply select the 'Run All' command from the menu 'Code/Run Region' once the file has been opened. In R, type source('PaCeQuantEval.R') at the input prompt. 5. After termination all plots can be found in the specified output directory. ---- Enjoy PaCeQuant!