ashenoy-cmbi/grafify: Version 2.3.0

The main motivation behind this update was to simplify the package by reducing the number of exported functions. So some features that were previously in separate functions have been made available more easily via an additional argument to existing functions (e.g. single colour function (plot_..._sc) now offered in respective plot_ function with a new argument (see below). This has uncluttered the namespace of grafify. Most of the other additions are related to colour schemes.

1. A new SingleColour argument has been added to two-variables plot_ functions to generate graphs with a single colour along the X-axis aesthetic. This means the 8 plot_..._sc functions introduced in v1.5.0 are deprecated, but this feature is still retained in existing plot_ functions. This option also added to plot_3d_ functions for plots of one-way ANOVA data.

2. Four new colourblind-friendly categorical colour schemes (chosen from cols4all package):

• fishy, kelly, r4, safe

1. Four new quantitative schemes for continuous or divergent colours.

• sequential/continuous: blue_conti, grey_conti
• divergent: OrBl_div, PrGn_div

All schemes also available through scale_fill.. and scale_colour_... calls to be used on any ggplot2 object.

1. scale_fill_grafify and scale_colour_grafify (or scale_color_grafify) have been rewritten. These have two new arguments that offer features previously in scale_fill_grafify2/scale_colour_grafify2/ scale_color_grafify_c and scale_fill_grafify_c/scale_colour_grafify_c/ scale_color_grafify_C scale functions. These 6 functions are now deprecated to reduce exported namespace.

The new arguments are discrete (logical T/F) to select discrete or continuous palettes, and ColSeq (logical T/F) to pick sequential or distant colours from a chosen palette.

1. Fixed the error in legend title in one-way ANOVA plots with plot_3d_ that incorrectly referred to xcol and shapes arguments.
2. Fixed the error that led to depiction of different shapes in plot_3d_scatterviolin as compared to the other two plot_3d_ functions.
3. posthoc_Trends... functions rewritten with stats::model.frame() to get model data frame as this is a more flexible method.
4. Order of colours in light, bright and muted schemes changed slightly for better separation of colours when next to each other.
5. The jitter setting in plot_scaltter_ is set to 0.2 so the graph as plotted with jitter by default.
6. The default colour scheme for all graphs is now okabe_ito (the all_grafify palette is was just a concatenation of all palettes without real basis in good visualisation). Use one of the other palettes if more than 8 colours are needed (e.g. kelly, which has 20 discreet colours).