NEWS.md
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.
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.
Four new colourblind-friendly categorical colour schemes (chosen from cols4all package):
fishy
, kelly
, r4
, safe
blue_conti
, grey_conti
OrBl_div
, PrGn_div
All schemes also available through scale_fill..
and scale_colour_...
calls to be used on any ggplot2
object.
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.
plot_3d_
that incorrectly referred to xcol
and shapes
arguments.plot_3d_scatterviolin
as compared to the other two plot_3d_
functions.posthoc_Trends...
functions rewritten with stats::model.frame()
to get model data frame as this is a more flexible method.light
, bright
and muted
schemes changed slightly for better separation of colours when next to each other.jitter
setting in plot_scaltter_
is set to 0.2
so the graph as plotted with jitter by default.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).This is a major update with some new features, bugfixes, and further cleaning up of code with consistent names of arguments in preparation for CRAN submission. Some previous code may not work because of renaming of some arguments for grouping variables in plot_
functions. But older arguments are retained with deprecation warnings in most cases, so old code should largely work.
plot_
functions have a new argument ColSeq
(logical TRUE/FALSE) that picks colours sequentially from palette chosen by ColPal
when TRUE
(default). If set to FALSE
, the most distant colours are chosen, as already implemented in scale_..._grafify2
functions.geom_violin
. They also get new arguments to set thickness of lines (bvthick
) and transparency of boxplots (b_alpha
).mixed_model_slopes
and mixed_anova_slopes
.posthoc_Trends
implements the emmeans::emtrends
call.plot_
functions now have the ...
argument forwarding dots for advanced users to add arguments to ggplot
geometries where necessary.plot_grafify_palette
function that helps quickly visualise colours in palettes along with their names and hexcodes.plot_bar_sd
and plot_bar_sd_sc
have a new argument bthick
to adjust the thickness of lines of the bars.Group
grouping argument in plot_density
, plot_histogram
and plot_qqline
is now called group
for consistency with other plot_
functions.Factor
argument in post-hoc comparisons functions (posthoc_Pairwise
, posthoc_vsRes
, and posthoc_Levelwise
) renamed as Fixed_Factor
to be consistent with mixed_model
, simple_model
, mixed_anova
and simple_anova
functions.plot_3d_scatterbar
and plot_3d_scatterbox
now correctly plot one-way ANOVA designs with randomised blocks with shapes
mapped to levels of the random factor, and xcol
as the grouping factor as originally intended but incorrectly implemented. This complements plot_4d_scatterbar
and plot_4d_scatterbox
which take two grouping factors and a random factor.groups
in before-after plots is now called match
as it is a bit more informative when showing matched data.c_alpha
in plot_density
and plot_histogram
(for colour opacity of colours under the density curve or histogram); opacity of symbols in plot_qqline
is still called s_alpha
.This update fixes and cleans up code to remove all errors, warnings and notes from devtools::check()
. All previous code should still work.
broom.mixed::augment
is used to get model residuals than the fortify
method as this will be deprecated soon. The broom.mixed
package therefore required.lmerTest
, but instead forces a mixed model object as lmerModLmerTest
object to get F and P values in ANOVA tables from the stats::anova
call.magrittr
package is required for internal use of pipes (%>%
).simple_model
and mixed_model
was cleaned up so that model outputs are as close to objects generated by native calls to lm
or lmer
.make_1w_rb_data
and make_2w_rb_data
functions have been updated to have consistent factor and level names.This version has 8 new plot_
functions ending in _sc
for plotting data with two variables wherein the X variable is plotted in a single colour. This contrasts existing versions that plot the X variable with multiple colours chosen from the all_grafify
palette. This is convenient when there are too many groups on the X axis and multiple colours are not necessary.
plot_qqmodel
will plot a diagnostic Q-Q plot of a simple linear model (generated with simple_model
or lm
) or mixed effects linear model (generated with mixed_model
or lmer
) in a single step.
This version “breaks” a few arguments from v0.3.1, therefore is v1.4.1. Specifically, opacity for both symbols and bars/boxes/violins can be set using s_alpha
and b_alpha
or v_alpha
, respectively; previously, only bars/boxes/violin opacity could be set with a single alpha
parameter. Old code with just alpha
will no longer work, sorry! There are also new graph types and arguments for ANOVAs as below.
New graph types
plot_density
and plot_histogram
for smooth density or histogram plots through geom_density
and geom_histogram
respectively.plot_scatterbox
and plot_scatterviolin
that complement the plot_dot...
versions and instead use geom_point
with position_jitter
. These versions are useful when a large number of data points are needed to be plotted.Updates
simple_anova
where the table also has Mean SS.mixed_anova
now has two new arguments, one to change method for Df calculation and second to get type I or III SS (default is type II).jitter
argument added to plot_3d..
and plot_4d..
functions for consistency with other scatter plots.bwid
argument (for adjusting width of bars) added to plot_scatterbar_sd
for consistency.Bug fixes in mixed_model
and simple_model
which now correctly lists the data used in the call field.
plot_4d_scatterbar
function which is like plot_4d_scatterbox
but plots bar and SD. So there are now two plot_3d_
and plot_4d_
functions.TextXAngle
argument to prevent overlap.plot_dot_
functions now have dotthick
option to set stroke thickness. This is similar to symthick
for scatter/jitter plots.facet_wrap
or facet_grid
will not draw a box around panel text (unlike the default in theme_classic()
).plot_3d_
and plot_4d_
functions draw symbols in black colour.plot_3d_scatterbar
and plot_3d_scatterbox
, which now correctly use the “shapes” variable to fill colour of bars/boxes and shape of the symbols; symbols are depicted in black.simple_anova
generates type II ANOVA table through car::Anova()
, so the car
package is now a dependency. v0.1.0 and v0.2.0 generated type I ANOVA table through stats::anova()
.plot_
functions apply the all_grafify
colour scheme by default (see plot_
vignettes on how to change colours)plot_xy_NumGroup
) or categorical (plot_xy_CatGroup
).scale_fill_grafify_c
and scale_colour_grafify_c
), based on Paul Tol’s variant of YlOrBl scheme.