ashenoy-cmbi/grafify: Version 3.2.0

grafify v3.2.0 Major updates

1. theme_grafify updates:

   a. lineend = square as default for better-looking origin b. transparent backgrounds throughout the plot c. this theme is now applied to all grafify plots by default d. all text size on the graph is now the same as the basesize (default 20)

2. New arguments in violin plots (plot_dotviolin, plot_scatterviolin, plot_3d_scatterviolin and plot_4d_scatterviolin): two separate arguments bthick and vthick to set the line widths of the boxes and violins, respectively. The previous bvthick will still work, so if a value is provided that will be used for line widths of both boxes and violins.

3. New argument for two-way ANOVA graphs (plot_4d_): the group_wid can be used to change the space between groups along the X-axis (i.e., dodge width). Default group_wid = 0.8 will produce graphs that look similar to those in previous versions of grafify. If group_wid is set to 0, there will be no dodging of the factors along X-axis.

4. New arguments in before-after plots (i.e., plot_befafter_): bthick and lthick arguments can change line and box line widths independently.

1. For consistency, the default width (bwid argument) of bars and boxes in plot_4d_ functions is set as 0.7.
2. Parts of code rewritten for many plot functions to make them shorter and simpler.
3. log10 tick marks: a. In all plot_ functions: the tick marks now scale with the fontsize parameter. Previously, the sizes were set to "cm" units, which did not scale correctly. The long tick mark, middle and short ticks are sized: 7*fontsize/22, 4*fontsize/22 and 4*fontsize/22, respectively (note that the short and mid are the same size). The size (line width) equals fontsize/22, which is the same throughout grafify. b. For consistency and usefulness, the plot_logscales function also has the above defaults and now has fontsize = 20 as an additional argument and sizes scale accordingly. c. Colour of log10 tick marks have the same colour as ticks on non-transformed axis (grey20).