across our everlasting journey in bioinformatics, data visualization can eat up a significant portion of our time and efforts (and is also a major source of procrastination opportunities). Over time, one can discover certain tools which turn out to be of great help in facilitating the preparation of figures (whose statistical and aesthetic quality is continually increasing in publications).
So, I wanted ask/start a discussion on examples of tools or organization techniques which you have incorporated into your routines and have helped you be much more productive in the generation of figures in our field. I’m talking more about unspecific tools rather than specific visualizations. For instance, here are 2 examples which have helped me a lot and I have since continually used in figure preparation, in the context of using
ggplot2 to plot data:
- Using tools to produce perfectly-aligned and same-size plots: even when using the same graphics device size, ggplots are often squeezed to different sizes because of the figure labels, etc. Plots can be aligned with e.g. the
gridExtrapackages to avoid this problem (ref1).
- Using tools to rasterize plots with lots of data elements: for example, plotting a scatter plot with thousands of points (and not wanting to do a smoothed/2D density plot) will generate PDF images which take a long time to renderize. Packages like
ggrastr(ref2) can rasterize parts of plots while keeping others in vector format; or
ComplexHeatmapfor heatmaps specifically (ref3).
- Using graphical tools for post-editing of vector figures: when there is no solution at the programming level, e.g. Inkscape.
which tools, organization tricks, educational resources, are you particularly fond of, or routinely use, to help you to produce publication-quality figures?