Full reference to all functions available at grafify
GitHub pages.
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,
safeblue_conti,
grey_contiOrBl_div, PrGn_divAll 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).plot_3d_scatterviolin and
plot_4d_scatterviolin for one-way or two-way ANOVA design
data to plot scatter plots with violins with box and whiskers.
plot_qqmodel no longer relies on
broom.mixed; instead uses rstudent from the
base stats package to generate studentized residuals from a
model.
New experimental functions to compare slopes of linear regression via
posthoc_Trends_Pairwise,
posthoc_Trends_Levelwise and
posthoc_Trends_vsRef.
Minor changes to plot_qqmodel and
plot_qqline to fix some OS-specific errors. QQ plots by
default will have ok_orange colour within symbols when only
one level is present within group. Both functions now use
geom_qq and geom_qq_line (instead of
stat_qq and stat_qq_line) internally.
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.
Fixed a typo in posthoc_Levelwise where the
adjust argument was not being correctly passed on to
emmeans.
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.First release.