grafify - v5.0.0

grafify v5.0.0

Major updates

This version has major updates to linear mixed effects models functions (mixed_model, mixed_anova, mixed_model_slopes, mixed_anova_slopes). The other major updates are to plot_density and plot_histogram, which can now plot probability density, counts or normalised counts (only latter two options for histograms). Most old code should still work, but care is needed if arguments are not explicitly called. Changes as follows:

Updates to mixed_model, mixed_anova, mixed_model_slopes, mixed_anova_slopes:

a. All functions now have a new argument AvgRF, which is set to TRUE by default. This means that values of the response variable (Y_value) are averaged before a linear mixed effects model is fitted. This avoids pseudoreplication if there are multiple 'technical replicates' within levels of the Random_Factor. For behaviour like before (v4.0.1 or lower), set AvgRF = FALSE. b. The Formula argument allows the user to directly provide a formula to lmer(), which may be useful in more complex scenarios (e.g., nested designs). This argument is available in mixed_model and mixed_anova functions. c. The following transformations can be called directly on x (where x is a numeric variable passed on to Y_value or Fixed_Factor: log(x), log(x + c), logit(x), log(x/100), sqrt() or exponents (e.g., (c)^2).
Updates to arguments in plot_density and plot_histogram:

a. both functions have a new argument PlotType to choose a type of data transformation, i.e., use ggplot2 defaults or plot counts or normalised counts. For plot_density, this argument can be Density (default), which plots the smooth probability density curve, Counts or Normalised counts. For plot_histogram, the default for this argument is Counts, which can be changed to Normalised counts. This is achieved by passing y = after_stat(count) or y = after_stat(count/max(count)) to geom_density or geom_histogram. b. both functions also can do "log10" and "log2" along the X-axis (for plotting on semi-log plots). For consistency with other plot_ functions in grafify, these arguments are LogYTrans, LogYBreaks, LogYLabels and LogYLimits. c. a SingleColour argument has been added to change colours when a grouping variable is missing, i.e., when the argument group is not provided with a value. If a value is provided, however, SingleColour is ignored and the ColPal value is applied.

Minor updates

In a couple of plot_.. functions, the LogYLabels argument was called Ylabels, which has now been deprecated for consistency (old code will still work).
Since ggplot2 v3.5, the discrete_scale() has been updated and an argument (scale_name) has been dropped. The scale_fill_grafify and scale_colour_grafify functions have been accordingly updated.
Updated documentation and corrected links to other packages and DOIs.
In plots that use geom_violin (i.e., plot_scatterviolin, plot_3d_scatterviolin and plot_4d_scatterviolin), drop = FALSE has been added to avoid throwing up errors. Be careful if you have fewer than 2 data points.

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Published by ashenoy-cmbi 12 months ago

grafify - Version 4.0.1

grafify v4.0.1

This is a minor update to fix tests that were failing after an update to ggplot2 to version 3.5.0.

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Published by ashenoy-cmbi almost 2 years ago

grafify - Version 4.0

grafify v4.0

The reason this is a major update is that now ggplot2 version 3.4.0 or higher is required to avoid errors with grafify. The main difference is that size argument for line widths has been updated to linewidth.

Major updates

It is easier to plot 2-way ANOVA designs with or without blocking factors in this version with the following updates. There are two new plot_... functions for 1-way and 2-way designs.

a. plot_4d_ functions can now plot 2-way ANOVAs even if the shapes argument is not provided. Graph is plotted with shape = 21 as default.

b. plot_4d_point_sd and plot_3d_point_sd functions for plotting 2-way and 1-way ANOVAs without or with blocking factors as mean and SD/SEM/CI95 error bars.

Minor updates

Fixed the double {{ in theme_grafify.
Added hjust and vjust arguments to theme_grafify to adjust text alignment when angles are changed.
Several tests were rewritten to comply with ggplot2 update.

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Published by ashenoy-cmbi over 2 years ago

grafify - Version 3.2.0

grafify v3.2.0

Major updates

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

Minor updates

For consistency, the default width (bwid argument) of bars and boxes in plot_4d_ functions is set as 0.7.
Parts of code rewritten for many plot functions to make them shorter and simpler.
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).

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Published by ashenoy-cmbi almost 3 years ago

grafify - Version 3.1.0

grafify v3.1.0

New functionalities

plot_point_sd now allows all data points to be shown. All points will be plotted with geom_point if the all_alpha setting (opacity for all symbols) is set >0 (it is set to 0 so default graphs will only show the mean of all values). There are also options for all_size and all_jitter to adjust size and overlap.
SD, SEM or CI95 error bars are now possible through the ErrorType argument (default is "SD" error bars) in plot_dotbar_sd, plot_scatterbar_sd, plot_point_sd, plot_3d_scatterbar and plot_4d_scatterbar.

Minor updates

Y-axis labels fixed for plot_lm_predict which used to label Y-axis as pred rather than the correct name of the plotted variable.
Fixed the example for theme_grafify.
Re-written plog_qqline based on stat_qq and stat_qqline.
Also re-written plot_histogram which was throwing up warning messages after ggplot2 update. For uniformity with other grafify graphs, histograms now have a black border (like symbol borders in dot/scatter plots).
groups argument, which was deprecated several versions before, has been removed from before-after functions.
plot_bar_sd deprecated as similar graphs can be plotted with plot_scatterbar_sd with s_alpha = 0.
Fixed an error in scale_colour_grafify, which broke in v3.0.0.
SingleColour argument can now take base R colour names (e.g., "grey25") in addition to previously available options.
plot_grafify_palette can now also plot the quantitative colour schemes.

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Published by ashenoy-cmbi about 3 years ago

grafify - Version 3.0.0

grafify v3.0.0

Major updates

This is a major update for grafify, which now provides wrappers for basic generalised additive models (gam) through the mgcv package. There are a more plot_ functions, a grafify theme for ggplot objects, and simple data wrangling before plotting.

Major additions

Fit generalised additive models (gam) and get ANOVA tables with two new functions: ga_model and ga_anova. These are mainly for time-series analyses or where an assumption of linear relationship between predictor and outcomes is absent straight lines are not appropriate. Factor-wise smooths are fit with the by argument in mgcv, without or with a random factor. Random factors are also allowed with smooth re smooth. See documentation for mgcv smooths. Model diagnostics can be done with plot_qq_gam and plot_qq_model. Example data included as data_zooplankton is from Lathro RC, 2000.
All plot_ functions now have two major updates:

a. Log-transformation of axes: Axes can be transformed with log10 or log2 with LogYTrans and LogXTrans arguments. X axis transformations are only available for plot_xy_CatGroup and plot_xy_NumGroup. With log10 transformation, log-ticks will also appear. Default axes limits and labels should work in most cases, but if needed, three additional arguments are available: LogYBreaks, LogYLimits and LogYLabels (and respective ones for the X axis). b. facet argument to add another variable to created faceted plots with the facet_wrap layer in ggplot2. A related argument facet_scales can be used to set Y or X axis scales on faceted panels.

New plot functions:

a. plot_befafter_box is a new before-after plot function that includes a box and whisker plot to show data distribution in addition to lines joining matched data. In addition, both plot_befafter_colour and plot_befafter_shapes offer a box and whiskers summary of data.

b. plot_lm_predict and plot_gam_predict can be used to plot observed (raw) data and predicted data from fitted linear models.

c. plot_logscales is a function to easily perform "log10" or "log2" transformation on X or Y axes of any ggplot2 object along with log-ticks.

Table manipulations:

a. table_x_reorder is a function to reorder levels within a categorical variable. This uses factor from base R stats package to convert a column into a factor and reorders it based on a user-provided vector of group names.

b. table_summary is a wrapper around aggregate (base R) function, which gives mean, median, SD, and counts grouped by one or more variables.

A grafify theme for ggplot2: theme_grafify is a modification of theme_classic for making publication-ready grafify-like graphs easily when using ggplot2.

Minor changes

Much of the code has been edited and cleaned up. Among the main change is dropping unnecessary double curly brackets {{ }} within plot_ wrappers.

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Published by ashenoy-cmbi over 3 years ago

grafify - Version 2.3.0

grafify v2.3.0

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.

Major additions

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

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.

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.

Minor changes & bug fixes

Fixed the error in legend title in one-way ANOVA plots with plot_3d_ that incorrectly referred to xcol and shapes arguments.
Fixed the error that led to depiction of different shapes in 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.
Order of colours in light, bright and muted schemes changed slightly for better separation of colours when next to each other.
The jitter setting in plot_scaltter_ is set to 0.2 so the graph as plotted with jitter by default.
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).

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Published by ashenoy-cmbi over 3 years ago

grafify - Release v2.2.0

grafify v2.2.0

New features

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.

Minor fixes

plot_qqmodel no longer relies on broom.mixed; instead uses rstudent from the base stats package to generate studentized residuals from a model.

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Published by ashenoy-cmbi almost 4 years ago

grafify - Version v2.1.0

grafify v2.1.0

New features

New experimental functions to compare slopes of linear regression via posthocTrendsPairwise, posthocTrendsLevelwise and posthocTrendsvsRef.

Minor fixes

Minor changes to plotqqmodel and plotqqline to fix some OS-specific errors. QQ plots by default will have okorange colour within symbols when only one level is present within group. Both functions now use geomqq and geomqqline (instead of statqq and statqq_line) internally.

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Published by ashenoy-cmbi about 4 years ago

grafify - Version v2.0.0

grafify v2.0.0

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.

New features:

a. 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. b. Violin plots get a major face-lift with a box-whiskers plot on top of the violin. This gives a clearer picture of data and dispersion than the default quantile lines in geom_violin. They also get new arguments to set thickness of lines (bvthick) and transparency of boxplots (b_alpha). c. There are new functions for fitting linear models with varying slopes and intercepts. These are mixed_model_slopes and mixed_anova_slopes. d. A function for comparing slopes of linear fits posthoc_Trends implements the emmeans::emtrends call.
e. Most plot_ functions now have the ... argument forwarding dots for advanced users to add arguments to ggplot geometries where necessary. f. New plot_grafify_palette function that helps quickly visualise colours in palettes along with their names and hexcodes. g. plot_bar_sd and plot_bar_sd_sc have a new argument bthick to adjust the thickness of lines of the bars.

Bug fixes

a. Distribution plots: the The Group grouping argument in plot_density, plot_histogram and plot_qqline is now called group for consistency with other plot_ functions. c. The 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. d. The 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. e. Examples in help files have arguments explicitly labelled to make them easier to follow. f. groups in before-after plots is now called match as it is a bit more informative when showing matched data. g. For consistency, the argument for controlling opacity in distribution plots is renamed 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.

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Published by ashenoy-cmbi about 4 years ago

grafify - v1.5.1

v1.5.1

This update fixes and cleans up code to remove all errors, warnings and notes from devtools::check(). All previous code should still work.

a. The main update is that 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. b. The way ANOVA table is generated no longer relies on an internal function from 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. c. The magrittr package is required for internal use of pipes (%>%). d. Much of the code for 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. e. Several internal functions related to the colour palettes have now been exported as this was easier. f. The make_1w_rb_data and make_2w_rb_data functions have been updated to have consistent factor and level names.

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Published by ashenoy-cmbi about 4 years ago

grafify -

New in v1.5.0

New graph types 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 allgrafify palette. This is convenient when there are too many groups on the X axis and multiple colours are not necessary.
Plotting Q-Q plot of model residuals plotqqmodel will plot a diagnostic Q-Q plot of a simple linear model (generated with simplemodel or lm) or mixed effects linear model (generated with mixed_model or lmer) in a single step.
Minor fixes Fixed a typo in posthoc_Levelwise where the adjust argument wasn not being correctly passed on to emmeans.

(There was an issue with tag 1.5.0, so this is an updated tag 1.5.0.0 only.)

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Published by ashenoy-cmbi about 4 years ago

grafify - Version 1.4.1 release on zenodo

This is v1.4.1 with a link to zenodo for DOI.

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Published by ashenoy-cmbi over 4 years ago

grafify - Version 1.4.1

New in v1.4.1

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

a. plot_density and plot_histogram for smooth density or histogram plots through geom_density and geom_histogram respectively. b. two new plot types 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

a. simple_anova where the table also has Mean SS. b. 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). c. jitter argument added to plot_3d.. and plot_4d.. functions for consistency with other scatter plots. d. bwid argument (for adjusting width of bars) added to plot_scatterbar_sd for consistency.

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Published by ashenoy-cmbi almost 5 years ago

grafify - Version 0.3.1

Minor bug fixes. Bug fixes in mixed_model and simple_model which now correctly lists the data used in the call field.