biouno/biology-data

Data for bioinformatics tools, including input, parameters, and other files

Biology Data

This is a repository to store input, parameters, trees and other files for biotechnology tools, like Beast, Best, Bucky, FigTree, MrBayes, Structure and so on.

MrBayes diagnostics plot R script

The script can be found in mrbayes/mrbayes_diagnostics_plots.r. Below you can find a brief introduction on how to use it.

Files

1. Save R script file (mrbayes_diagnostics_plots.r) to your results folder.
2. Save Mrbayes output files to results folder.

###System Setup

1. Ensure relevant R packages are installed
2. cd to the working directory.
3. Open R in command console by typing the path of the "bin" folder containing the "Rscript" application, the name of the R script file (eg mrbayes_diagnostics_plots.r), and then -h.

e.g. "C:\Program Files\R\bin\Rscript mrbayes_diagnostics_plots.r -h"

Or

Avoiding the inconvenience of type the bin path each time, add the bin path to the path variable list i.e. Select computer ->properties -> advanced settings-> environmental variables. Under "System variables double click the "Path" variable and add the path of the R "bin" folder the the "variable value" list. Ok all changes.

e.g. "Rscript mrbayes_diagnostics_plots.r -h"

###Running plots

Modify settings as appropriate, and enter.