plotxvg 1.0.0

Batch-generation of publication quality graphs.

plotXVG

Molecular simulation tools such as GROMACS routinely produce time-series of energies and other observables. To turn this data into publication quality figures a user can either use a (commercial) software package with a graphical user interface, often offering fine control and high-quality output, or write their own code to make plots using a scripting language. In the age of big data and machine learning it is often necessary to generate many graphs, be able to rapidly inspect them, and to make plots for manuscripts. This repository provides plotxvg, a simple Python tool built on the well-known matplotlib plotting library that will generate publication-quality graphics from, for instance, an energy calculation. This will allow users to rapidly and reproducibly generate series of graphics files without programming. Obviously, the tool is applicable to any kind of line graph data, not just that from molecular simulations.

Pip install plotXVG to your current python environment by running

python -m pip install plotxvg  

in the command line. Or, if preferred, you can clone this repository by running

git clone https://github.com/AlexandriaChemistry/plotXVG 

cd into it and then run

python -m pip install .  

Simple as that! In the plotXVG directory you can find a number of showcase illustrations along with descriptive text files found under tests/plotxvg_tests-output/ and can also easily be generated by running python test.py in the tests folder. Example xvg-files have been generated by GROMACS and Alexandria Chemistry Toolkit (ACT), which cen be found in their respective folders.

To use plotXVG, simply type plotxvg -f <filename>.xvg in the command line and it will generate a plot. Default setting is a scatterplot, if you want to generate a lineplot, add the linestyle flag along with a line argument, such as -ls solid. PlotXVG supports a number of flags, shown below.

plotXVG flags

options:
  -h, --help            show this help message and exit
  -f [FILENAME ...], --filename [FILENAME ...]
                        Filename(s) to read and plot
  -follow, --follow     Continuously update the plot by re-reading the input file(s)
  -debug, --debug       Turn on printing of debugging messages
  -font FONTNAME, --fontname FONTNAME
                        Font for all text.
  -alfs AXISLABELFONTSIZE, --axislabelfontsize AXISLABELFONTSIZE
                        Axis label font size, default 26
  -tfs TITLEFONTSIZE, --titlefontsize TITLEFONTSIZE
                        Title font size, set to zero for no title, default 30
  -lfs LEGENDFONTSIZE, --legendfontsize LEGENDFONTSIZE
                        Legend font size, set to zero for no legend, default 26
  -tickfs TICKFONTSIZE, --tickfontsize TICKFONTSIZE
                        Tick font size, default 24
  -ls LINESTYLE [LINESTYLE ...], --linestyle LINESTYLE [LINESTYLE ...]
                        What kind of line style: solid, dashed, dashdot, dotted
  -mk MARKER [MARKER ...], --marker MARKER [MARKER ...]
                        Use markers for data sets: o, +, x, <, >...
  -mksize MARKERSIZE, --markersize MARKERSIZE
                        Size of filled markers for data sets, default 10
  -mkwidth MARKEREDGEWIDTH, --markeredgewidth MARKEREDGEWIDTH
                        Size of character markers (e.g. +) for data sets, default 2
  -colors [COLORS ...], --colors [COLORS ...]
                        Colors for the plots. Colors defined by the user will be applied to the datasets in order. If there are more datasets than color inputs, default colors will be
                        used.
  -save SAVE, --save SAVE
                        Save plot. Please specify saving location and preferred filetype (.pdf, .png...)
  -sqfig, --squarefig   Make the figure square
  -eqax, --equalaxes    Make the plot square with equally large axes
  -bar, --bar           Make a bar graph
  -noshow, --noshow     Do not show the figure
  -res, --residual      Subtract x from y for all data sets - useful for correlation plots
  -fl, --filelabel      Add the filename to the labels in the plot (may yield long labels)
  -logy, --logy         Use a log scale on the Y-axis
  -xmin XMIN, --xmin XMIN
                        Minimum value of X-axis. Default = defined by data.
  -xmax XMAX, --xmax XMAX
                        Maximum value of X-axis. Default = defined by data.
  -ymin YMIN, --ymin YMIN
                        Minimum value of Y-axis. Default = defined by data.
  -ymax YMAX, --ymax YMAX
                        Maximum value of Y-axis. Default = defined by data.
  -xframe XFRAME, --xframe XFRAME
                        Width of the plot 100 pixels, default 16
  -yframe YFRAME, --yframe YFRAME
                        Height of the plot 100 pixels, default 9
  -panels [{top,side}], --panels [{top,side}]
                        Generate different panels to plot in, one file per panel. Add 'side' for side-by side panels.
  -sfx SUBFIGUREX, --subfigureX SUBFIGUREX
                        X position of subfigure label when using panels. Default -0.15
  -sfy SUBFIGUREY, --subfigureY SUBFIGUREY
                        Y position of subfigure label when using panels. Default 1.0
  -ign [IGNORE ...], --ignore [IGNORE ...]
                        legends of the series to ignore. Please specify the whole legend label.
  -title TITLE [TITLE ...], --title TITLE [TITLE ...]
                        User-defined title(s). This flag overwrites pre-defined titles. If the user wants to use user-defined titles and pre-defined titles on different panels, use None
                        as placeholders for predefnied title panels. If the user wants to remove a specific panel title, put an empty string ''.
  -notitles, --notitles
                        Remove all titles (Both user-defined and title pre-defined by data.)
  -dslegends [DATASETLEGENDS ...], --datasetlegends [DATASETLEGENDS ...]
                        Set user-defined legends. If legends are already defined in the input file they are combined for each dataset i.e. '<user-defined legend> <pre-defined legend>'.
  -sharelabel, --sharelabel
                        Show only the x-labels on the last row of plots and the y-labels on the first column of plots (useful if all subplots share the same x- and y-labels)
  -legend_x LEGEND_X, --legend_x LEGEND_X
                        Put the legend box horizontally on this position, default 0.02
  -legend_y LEGEND_Y, --legend_y LEGEND_Y
                        Put the legend box vertically on this position, default 0.98
  -stats, --stats       Print RMSD and R2 values of datasets (x-axis is reference data and y-axis holds the predicted values)
  -csvx CSVX, --csvx CSVX
                        Choose what x column you would like from a csv file. Choose only one column. Default is column 1
  -csvy CSVY [CSVY ...], --csvy CSVY [CSVY ...]
                        Choose what y column(s) you would like from a csv file. Default is column 3