Those settings which are expected to vary from one sample to the next, such as the minimum and maximum values of the horizontal axis, bandwidth, binwidth and central value, can be accessed from the command line. Other properties, which apply to multiple samples, such as colour settings and data transformations, are stored in the preferences file (.densityplotter or .radialplotter) and cannot be accessed from the command line. Together, the preferences file and the command line allow the user to access all of the functionality of the program in batch mode. Here are some examples of command line instructions:

java -jar path-to-program/DensityPlotter.jar, or: java -jar path-to-program/RadialPlotter.jar

to which the following optional flags can be added:

in=path-to-file/input.csv loads input.csv into the program. out=path-to-file/output.pdf saves the graphical output to a file named output.pdf and exits the program afterwards. min=tm sets the minimum limit of the x-axis (density plots) and radial scale (radial plots) to tm. max=tM sets the maximum limit of the x-axis (density plots) and radial scale (radial plots) to tM. central=tc sets the central value of the radial scale to tc. binwidth=width sets the binwidth of the sample histogram. bandwidth=width sets the bandwidth of the Kernel Density Estimator. markers="n1,n2,n3" adds marker lines at positions n1, n2 and n3. numpeaks=n fits n peaks to the data, where n is an integer number between 1 and 5 (to model a finite mixture of discrete components), OR a negative number (to determine the minimum age).

Examples:

java -jar RadialPlotter.jar in=/home/pieter/Namibia/NAM01.csv → Open NAM01.csv in RadialPlotter. java -jar DensityPlotter.jar min=0 max=1000 in=/home/pieter/Namibia/NAM01.csv out=/home/pieter/Desktop/NAM01dens.pdf → Open NAM01.csv in DensityPlotter, set the x-axis limits from 0 to 1000, and save the plot on the Desktop as NAM01dens.pdf java -jar "/home/pieter/Programming/DensityPlotter/DensityPlotter.2.2.jar" binwidth=10 bandwidth=10 in=UPbdata.csv out=UPbdata.png → Open UPbdata.pdf in legacy version DensityPlotter.2.2.jar, set the histogram binwidth and KDE bandwidth to 10, send output to UPbdata.png java -jar RadialPlotter.jar min=10 max=500 central=150 in=NAM02.csv → Open NAM02.csv in RadialPlotter, set the minimum value of the radial scale to 10, the central value to 150 and the maximum to 500.

Combining such commands in a batch file enables quick processing of large numbers of data files.