Graphical tools

Fra Robin

Versjonen fra 16. sep 2021 kl. 16:21

Figures/Illustrations

• Vector Graphics Editors
  • Inkscape (free and open-source)
  • Adobe Illustrator (for students only through UiO programkiosk)
  • Directly in LaTeX (PGF/TikZ: https://github.com/pgf-tikz/pgf; some examples)
  • LibreOffice Draw (free and open-source)
  • Through presentation software such as Powerpoint, Keynote, …
  • Web-based options: Google draw (in Google disk), Draw.io, Figma, Lucid charts, …

• Raster Graphics Editors
  • Gimp (free and open-source)
  • Adobe Photoshop (for students only through UiO programkiosk)
  • Photopea (online editor)

• 3D Computer Graphics Editors
  • Blender (free and open-source)
  • Autodesk Maya
  • see also here

Plotting Apps

• Python
  • Matplotlib
    • see Mouret's tutorial for publication quality plots
    • check the cheat sheets 1 & 2
  • Seaborn (statistical data visualization; uses Matplotlib internally. See for example this tutorial)
• R
  • ggplot2 (with Rstudio)
• Matlab (available at UiO)
• Octave (free alternative to matlab)
• Gnuplot
• Desmos.com (web based)
• javaFX
• excel (UiO)

Digitalize Figures

To qualitatively compare one's own data with other published data, it is sometimes needed to obtain the concrete data of the respective publication. In that case there are multiple ways to do that:

• Python: https://github.com/dilawar/PlotDigitizer
• Matlab: https://blogs.mathworks.com/steve/2013/12/31/automating-data-extraction-1/
• External App: WebPlotDigitizer

Tips on Exporting Figures

• Before saving the graphics in the respective programs
  • Avoid bitmap graphics if possible and especially jpg!
  • Preferably use vector graphics such as svg, pdf or eps (can be edited with vector graphics editors)
  • Check your colour maps! (see https://www.nature.com/articles/s41467-020-19160-7 or https://matplotlib.org/stable/tutorials/colors/colormaps.html)
  • Check font size, font type, line widths, marker sizes, proportions, aspect ratios and resolution!
  • Example plots with mostly default (left) and adapted (right) plotting parameters.
  • 
• Sometimes it is neccessary to use png format (e.g. in case of render graphics or plots with an essential transparency effect)
  • In that case, one should pick a proper resolution for the export file while accounting for its file size
  • Possible ways to compress the png file is to use for example pngquant, AdvanceCOMP or ImageMagick
• Exporting to LaTeX
  • Recommended approach:
    • export as pdf
    • optionally use pdfcrop (usually installed with LaTeX) to cut unecessary white space
    • in case only eps export is supported, use epstopdf (usually installed with LaTeX)
  • For direct inclusion in LaTeX, use the following scripts to create PGF/TikZ files:
    • Python: https://github.com/nschloe/tikzplotlib
    • R: https://github.com/daqana/tikzDevice
    • Matlab/Octave: https://github.com/matlab2tikz/matlab2tikz
  • It is possible to either input the code directly through \input{} or to compile the figure first through the standalone class