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ggadjust_pvalue() added to adjust p-values
produced by geom_pwc() on a ggplot (#522).gene_expressionggpubr.null_device, which value should be a function that
creates an appropriate null device. These include:
cowplot::pdf_null_device,
cowplot::png_null_device,
cowplot::cairo_null_device and
cowplot::agg_null_device. Default is
cowplot::pdf_null_device. This is used in function like
as_ggplot(), which needs to open a graphics device to
render ggplot objects into grid graphics objects. This function is used
to open null device for avoiding the display of unnecessary blank page
when calling ggarrange() or as_ggplot() (#306
and #158). The default option can be changed using, for example,
options(ggpubr.null_device = cowplot::png_null_device).gadd(): Restoring back random state after setting seed
when adding jittered points. To do so, the seed number is just passed to
position_jitter() and position_jitterdodge(),
which preserve the initial random state ( #177 and #349) .ggpubr requires now a version of
ggrepel >= 0.9.2.9999, which restores now the initial
random state after set.seed(). see
https://github.com/slowkow/ggrepel/issues/228ggpubr requires now a version of
cowplot >= 1.1.1ggtexttable(): doc updated with another example; text
justification for individual cells/rows/columns (#335).ggpie(): setting the default of
clip = "off" in coord_polar() so that
ggpie() does not crop labels (#429)as_ggplot(): using null_device to avoid blank page #306
and #158ggarrange(): using null_device to avoid blank page #306
and #158df is
a tibble.ggexport(): support added for graphics device svg
(#469)ggpie() and ggdonutchart() now fully
reacts to the option lab.font (#502)gather_() in both internal
(.check_data()) and exported functions
(compare_means()) (#513)stat_compare_means(): The dot-dot notation
(..p.signif..) was deprecated in ggplot2 3.4.0;
after_stat(p.signif) should be used; updated so that
..p.signif.. is automatically converted into
after_stat() format without warning for bacward
compatibility.desc_statby() doc updated to clarify the difference
between SD (standard deviation) and SE (standard error) (#492)geom_smooth() using formula 'y ~ x' is now
turned off in ggscatter()(#488)ggtext(): fix warning “filter_() was
deprecated in dplyr 0.7.0”.ggqqplot(): the argument conf.int is taken
into account now when specified (#524).ggqqplot(): Fixing the warning: “The following
aesthetics were dropped during statistical transformation: sample”
(#523)rstatix v >=0.7.1.999 for preserving
factor class in emmeans_test() (#386)ggmaplot(): Suppressing ggmaplot warning: Unlabeled
data points (too many overlaps). Consider increasing max.overlaps
(#520)compare_means(): works now when the grouping variable
levels contain the key words group2 or group1 (#450)ggparagraph() : fixing bug about minimum paragraph
length (#408)ggexport(): the verbose argument is now considered when
specifyed by user (#474)stat_anova_test(),
stat_kruskal_test(), stat_welch_anova_test(),
stat_friedman_test() and geom_pwc() added.
These are flexible functions to add p-values onto ggplot with more
options. The function geom_pwc() is for adding pairwise
comparisons p-values to a ggplot; supportted statistical methods include
“wilcox_test”, “t_test”, “sign_test”, “dunn_test”, “emmeans_test”,
“tukey_hsd” and “games_howell_test”.as_npc(), npc_to_data_coordinates() and
get_coord().ggpubr_options() to display allowed global
options in ggpubrggpubr.parse_aes.
logical indicating whether to parse or not the aesthetics variables
names. Default is TRUE. For example, if you want ggpubr to
handle non-standard column names, like A-A, without parsing, then set
this option to FALSE using
options(ggpubr.parse_aes = FALSE).stat_conf_ellipse: ensure stat returns a data.frame for
compatibility with ggplot2 v>=3.4.0stat_compare_means():
after_stat(p.signif) as the dot-dot
notation (..p.signif..) was deprecated in ggplot2 3.4.0
(#509).ggdensity() and gghistogram(): dot-dot
notation (..density.., ..count..) replaced by
after_stat(density) and after_stat(count),
respectively for compatibility with ggplot2 3.4.0.create_aes():
options(ggpubr.parse_aes = FALSE).digits and table.font.size)
added to ggsummarystats() for changing the summary table
decimal place and text size (#341).stat_pvalue_manual() the argument
hide.ns can be either a logical value (TRUE or FALSE) or a
character value (“p” or “p.adj” for filtering out non significant by
p-value or adjusted p-values).vjust = 0.5 (#301).Capital NS. is no longer displayed by
stat_compare_means() (#171)ggshistogram() to make sure that it
works when:
after_stat(),ggscatter() to make sure that:
ggpubr.parse_aes global option is set to FALSE (#229)ggtexttable() (#125,
#129 and #283):
tab_cell_crossout(): cross out a table cell.tab_ncol(), tab_nrow(): returns, respectively, the
number of columns and rows in a ggtexttable.tab_add_hline(): Creates horizontal lines or separators
at the top or the bottom side of a given specified row.tab_add_vline(): Creates vertical lines or separators
at the right or the left side of a given specified column.tab_add_border(), tbody_add_border(), thead_add_border():
Add borders to table; tbody is for table body and thead is for table
head.tab_add_title() and tab_add_footnote() to
add titles and footnotes (#243).create_aes() added to create aes mapping
from a list. Makes programming easy with ggplot2 (#229).coord.flip added to support adding
p-values onto horizontal ggplots (#179). When adding the p-values to a
horizontal ggplot (generated using coord_flip()), you need
to specify the option coord.flip = TRUE.median_hilow_() and
median_q1q3() - added (@davidlorenz,
#209):
median_hilow_(): computes the sample median and a
selected pair of outer quantiles having equal tail areas. This function
is a reformatted version of Hmisc::smedian.hilow(). The
confidence limits are computed as follow:
lower.limits = (1-ci)/2 percentiles;
upper.limits = (1+ci)/2 percentiles. By default
(ci = 0.95), the 2.5th and the 97.5th percentiles are used
as the lower and the upper confidence limits, respectively. If you want
to use the 25th and the 75th percentiles as the confidence limits, then
specify ci = 0.5 or use the function
median_q1q3().median_q1q3(): computes the sample median and, the 25th
and 75th percentiles. Wrapper around the function median_hilow_() using
ci = 0.5.get_breaks() added to easily create breaks
for numeric axes. Can be used to increase the number of x and y ticks by
specifying the option n. It’s also possible to control axis
breaks by specifying a step between ticks. For example, if by = 5, a
tick mark is shown on every 5 (@Chitanda-Satou,
#258).ggscatterhist() (@juliechevalier,
#176):
ggscatterhist() is now a list of ggplots,
containing the main scatter plot (sp) and the marginal
plots (xplot and yplot), which can be
customized by the end user using the standard ggplot verbsalternative supported in
stat_cor() (#276).position in ggline() to make
position “dodged” (#52).outlier.shape in ggboxplot(). Default is
19. To hide outlier, specify outlier.shape = NA. When jitter is added,
then outliers will be automatically hidden.ggdotchart() using the
option sorting = "none" (#115, #223).weight added in gghistogram()
for creating a weighted histogram (#215)ggscaterhist() takes into account the argument
position in margin.params when marginal plot
is a histogram (#286).ggbarplot() enhanced to better handle the creation of
dodged bar plots combined with jitter points (@aherholt, #176)bracket.shorten added in
stat_pvalue_manual() and geom_bracket(). a
small numeric value in [0-1] for shortening the with of bracket
(#285).bracket.nudge.y added in
stat_pvalue_manual() and geom_bracket().
Vertical adjustment to nudge brackets by. Useful to move up or move down
the bracket. If positive value, brackets will be moved up; if negative
value, brackets are moved down (#281).numeric.x.axis added in
ggerrorplot(); logical value, If TRUE, x axis will be
treated as numeric. Default is FALSE (#280).width is now considered in
ggadd() for plotting error bars (#278).linetype in ggpaired().geom_exec() used in ggpaired() to add
lines between paired points.ggmaplot() now supports two input formats (#198):
ggmaplot():
alpha for controlling point transparency/density (@apcamargo,
#152).label.select to select specific genes to show on the
plot (@apastore, #70)ggadd() the fill argument is considered
for jitter points only when the point shape is in 21:25 (@atakanekiz,
#148).parse added in ggscatter()
and in ggtext(). If TRUE, the labels will be parsed into
expressions and displayed as described in ?plotmath (#250).stroke supported in
ggscatter() and in ggline(). Used only for
shapes 21-24 to control the thickness of points border (@bioguy2018,
#258).stat_cor() function code has been simplified. New
arguments p.accuracy and r.accuracy added; a
real value specifying the number of decimal places of precision for the
p-value and the correlation coefficient, respectively. Default is NULL.
Use (e.g.) 0.01 to show 2 decimal places of precision (@garthtarr, #186, @raedevan6, #114, #270).annotate_figure() manual updated to show how to use of
superscript/subscript in the axis labels (#165).ggtextable() now supports further customization when
theme is specified (#283).font.family is now correctly handled by
ggscatter() (#149)ggpar() arguments are correctly applied using
ggpie() (#277).ggscatter(): When conf.int = FALSE, fill
color is set to “lightgray” for the regression line confidence band (@zhan6073, #111).gghistogram() supports the paramter
yticks.by (@Chitanda-Satou,
#258).ggsummarystats() to create a GGPLOT with summary stats
table under the plot ( #251).clean_table_theme() to clean the the theme of a table,
such as those created by ggsummarytable()ggbarplot() now supports stacked barplots with error
bars (#245).vjsut in stat_compare_means() to move the
text up or down relative to the bracket.type in geom_bracket() to specify label
type. Can be “text” or “expression” (for parsing plotmath expression);
#253.labeller to the function facet()position in get_legend() to specify legend
positionlegend.grob in ggarrange() to specify a
common legend you want to add onto the combined plot.cor.coef.name in the function
stat_cor(). Can be one of “R” (pearson coef), “rho”
(spearman coef) and “tau” (kendall coef). Uppercase and lowercase are
allowed (@andhamel, #216).digits, r.digits, p.digits in the
function stat_cor(). Integer indicating the number of
decimal places (round) or significant digits (signif) to be used for the
correlation coefficient and the p-value (@raedevan6,
#216).compare_means() adapted to tidyr v>= 1.0.0 by
specifying cols in the unnest() function (@Youguang, #216).stat_pvalue_manual() can now handle an rstatix test
result containing only one group column.stat_central_tendency() to add central
tendency measures (mean, median, mode) to density and histogram
plotsstat_overlay_normal_density() to overlay
normal density plot (with the same mean and SD) to the density
distribution of ‘x’.exact = FALSE is no longer used when
computing correlation in stat_cor() (@tiagochst,
#205)ggpie() keeps now the default order of labels (@WortJohn, #203)geom_bracket() for adding brackets with
label annotation to a ggplot. Helpers for adding p-value or significance
levels to a plot.compare_means() has been adapted to tidyr v1.0.0 (@jennybc, #196)geom_exec() now handles geom_bracket()
argumentsvjust, hide.ns,
step.increase, step.group.by,
color and linetype added in
stat_pvalue_manual()stat_pvalue_manual() can now guess automatically the
significance label column.show.legend added to ggadd()
and add_summary() functions.gghistogram(). Works now when the x
variable is R keyword, such as var, mean, etc. (#192)ggline(), error bars now react automatically to
grouping by line type (#191)step.increase added in
stat_compare_means() to avoid overlap between
brackets.stat_pvalue_manual() x axis variable is no longer
automatically converted into factor. If your x variable is a factor,
make sure that it is converted into factor.stat_pvalue_manual() can automatically handle the
output of rstatix testsggbarplot() and ggviolin() now
automatically create error bars by groups when users forget the option
add.params = list(group = ) (#183).ggarrange() works when either
ncol = 1 or nrow = 1 (@GegznaV, #141.compare_means() set automatically the option
exact = FALSE. This is no longer the case (@stemicha, #141.stat_pvalue_manual() now supports dodged grouped plots
(@emcnerny, #104).position is now handled by
ggdotplot() (@Adam-JJJJJ,
#178)label.sep argument works now in
ggscatter() and stat_cor() (@sbbmu, #150)ggscatter() to avoid freezing when the
add argument is incorrect (@atakanekiz,
#135).The option ref.group was only considered when the
grouping variable contains more than two levels. In that case, each
level is compared against the specified reference group. Now,
ref.group option is also considereded in two samples mean
comparisons (@OwenDonohoe,
#118)
Now, ggqqplot() reacts to the argument
conf.int.level (@vsluydts,
#123
Added error bar color is now inherited from the main plot (@JesseRop, #109
bxp.errorbar added to
ggboxplot() for adding error bars at the top of the box
plots (@j3ypi, #105.stat_pvalue_manual() for adding p-values
generated elswhere (@achamess, #81, @grst, #65).alphaoption added to ggviolin() @mtmatter, #77bracket.size added to
stat_compare_means() @mtmatter, #43stat_cor() supports R^2 as an option
@philament, #32position added in
gghistogram(). Allowed values include “identity”, “stack”,
“dodge”.ci added in ggerrorplot() @abrar-alshaer,
#94ggscatter() can remove the letter ‘a’ from the
legend, when the argument show.legend.text = FALSE
specified @atsyplenkov,
#106.size option to ggscatter
add.params is supported @retrogenomics,
#94.ggdonutchart() added.Significance levels can be now customized and passed to
stat_compare_means() (@jaison75,
#45).
Editing pdf size is now supported in ggexport() (@JauntyJJS,
#45).
ggscatterhist() the x variable was plotted two
times, on both the plot x & y margins, instead of having, as
expected, a) the x variable on the main plot x margin and 2) the y
variable on the main plot y margin. This has been now fixed.ggdotchart() sorted automatically
within groups when the color argument is specified, even
when groups = NULL. This default behaviour has been now removed. Sorting
withi groups is performed only when the argument group is
specified (@sfeds, #90).yticks.by and xticks.by work with NAs
(@j3ypi, #89).New function ggballoonplot() added to visualize a
contingency table.
ggdotchart() can be now used to plot multiple groups
with position = position_dodge() (@ManuelSpinola,
#45).
New function ggscatterhist() to create a scatter
plot with marginal histograms, density plots and box plots.
New theme theme_pubclean(): a clean theme without
axis lines, to direct more attention to the data.
New arguments in ggarrange() to customize plot
labels (@G-Thomson, #41):
New argument method.args added to
stat_compare_means(). A list of additional arguments used
for the test method. For example one might use method.args =
list(alternative = “greater”) for wilcoxon test (@Nicktz, #41).
New argument symnum.args added to
stat_compare_means(). A list of arguments to pass to the
function symnum for symbolic number coding of p-values. For example,
symnum.args <- list(cutpoints = c(0, 0.0001, 0.001, 0.01, 0.05, 1), symbols = c("****", "***", "**", "*", "ns"))
New functions table_cell_font() and
table_cell_bg() to easily access and change the text font
and the background of ggtexttable() cells (@ProbleMaker,
#29).
New argument numeric.x.axis in
ggline(). logical. If TRUE, x axis will be treated as
numeric. Default is FALSE. (@mdphan, #35)
New argument lab.nb.digits in
ggbarplot(). Integer indicating the number of decimal
places (round) to be used (#28). Example:
lab.nb.digits = 2.
New argument tip.length in
stat_compare_means(). Numeric vector with the fraction of
total height that the bar goes down to indicate the precise column.
Default is 0.03. Can be of same length as the number of comparisons to
adjust specifically the tip lenth of each comparison. For example
tip.length = c(0.01, 0.03).
get_legend() returns NULL when the plot doesn’t
have legend.Now data argument are supported in
stat_compare_means() when the option comparisons are
specified (@emcnerny,
#48)
Now compare_means() returns the same p-values as
stat_compare_means() (@wydty, #15).
stat_compare_means() now reacts to label =
“p.format” when comparisons specified (#28).
Now, the p.values are displayed correctly when ref.group is not the first group (@sehufnkjesktgna, #15).
In ggpar(), now legend.title can be
either a character vector, e.g.: legend.title = “Species” or a list,
legend.title = list(color = "Species", linetype = "Species", shape = "Species").
New argument ellipse.border.remove in
ggscatter() to remove ellipse border lines.
ggscatter(mtcars, x = "mpg", y = "wt",
color = "cyl",
ellipse = TRUE, mean.point = TRUE,
ellipse.border.remove = TRUE)In ggscatter(), the argument mean.point
now reacts to fill color.
Support for text justification added in
ggtexttable() (@cj-wilson,
#15)
The function ggpie() can now display japanese texts.
New argument font.family in ggpie() and in
ggpar() (@tomochan001,
#15).
Using time on x axis works know with ggline() and
ggbarplot() (@jcpsantiago,
#15).
stat_compare_means() now reacts to hide.ns
properly.drawDetails.splitText() exported so that the function
ggparagraph() works properly.ggbarplot(), now labels correspond to the true size
of bars (@tdelhomme,
#15).stat_compare_means() now keep the default order of
factor levels (@RoKant, #12).gradient_color() and gradient_color():
change gradient color and fill palettes.clean_theme(): remove axis lines, ticks, texts and
titles.get_legend(): to extract the legend labels from a
ggplot object.as_ggplot(): Transform the output of
gridExtra::arrangeGrob() and
gridExtra::grid.arrange() to a an object of class
ggplot.ggtexttable(): to draw a textual table.ggparagraph(): to draw a paragraph of text.annotate_figure() to annotate (arranged) ggplots.text_grob() to create easily a customized text
graphical object.background_image() to add a background image to a
ggplot.theme_transparent() to create a
ggplot with transparent background.gghistogram(), density curve and rug react to the
fill color.ggarrange():
àlign to specify whether graphs in the
grid should be horizontally (“h”) or vertically (“v”) aligned.legend to remove or specify the legend
position when arranging multiple plots.common.legend to create a common unique
legend for multiple plots.New functions:
ggarrange() to arrange multiple ggplots on the same
page.ggexport() to export one or multiple ggplots to a file
(pdf, eps, png, jpeg).ggpaired() to plot paired data.compare_means() to compare the means of two or multiple
groups. Returns a data frame.stat_compare_means() to add p-values and significance
levels to plots.stat_cor() to add correlation coefficients with
p-values to a scatter plot.stat_stars() to add stars to a scatter plot.Now, the argument y can be a character vector of
multiple variables to plot at once. This might be useful in genomic
fields to plot the gene expression levels of multiple genes at once. see
ggboxplot(), ggdotplot(),
ggstripchart(), ggviolin(),
ggbarplot() and ggline.
The argument x can be a vector of multiple variables
in gghistogram(), ggdensity(),
ggecdf() and ggqqplot().
New functions to edit ggplot graphical parameters:
font() to change the appearance of titles and
labels.rotate_x_text() and rotate_y_text() to
rotate x and y axis texts.rotate() to rotate a ggplot for creating horizontal
plot.set_palette() or change_palette() to
change a ggplot color palette.border() to add/change border lines around a
ggplot.bgcolor() to change ggplot panel background color.rremove() to remove a specific component from a
ggplot.grids() to add grid lines.xscale() and yscale() to change axis
scale.New helper functions:
facet() added to create multi-panel plots (#5).add_summary() to add summary statistics.ggadd() to add summary statistics or a geometry onto a
ggplot.New data set added: gene_citation
New arguments in ggpar(): x.text.angle
and y.text.angle
New arguments in ggpubr functions, see ggboxplot(),
ggdotplot(), ggstripchart(),
ggviolin(), ggbarplot() and
ggline:
combine added to combine multiple y variables on the
same graph.merge to merge multiple y variables in the same ploting
area.select to select which item to display.remove to remove a specific item from a plot.order to order plot items.label, font.label, label.select, repel, label.rectangle
to add and customize labelsfacet.by, panel.labs and short.panel.labs: support for
faceting and customization of plot panelsNew argument grouping.vars in ggtext().
Grouping variables to sort the data by, when the user wants to display
the top n up/down labels.
New arguments in theme_pubr():
palette Can be also a numeric vector
of length(groups); in this case a basic color palette is created using
the function grDevices::palette().Now, ggpar() reacts to palette when length(palette)
= 1 and palette is a color name #3.
ggmaplot() now handles situations, where there is
only upregulated, or downlegulated gnes.
get_palette() to generate a palette of k
colors from ggsci palettes, RColorbrewer palettes and custom color
palettes. Useful to extend RColorBrewer and ggsci to support more
colors.ggpar() function can handle a list of
ggplots.right.show.legend.text in the
ggscatter() function. Use show.legend.text = FALSE to hide
text in the legend.title, submain, subtitle, caption, font.submain, font.subtitle, font.caption
in the ggpar() function.font.family in
ggscatter().ggdensity
(gghistogram) are now shown if data have NA values @chunkaowang,
#1ggtext() for textual annotation.ggscatter(). A logical value.
If TRUE, a star plot is generated.geom_exec(). A helper function used
by ggpubr functions to execute any geom_xx functions in ggplot2. Useful
only when you want to call a geom_xx function without carrying about the
arguments to put in ggplot2::aes().ggbarplot().
theme_classic2() added. Classic theme with
axis lines.ggboxplot(), ggviolin(),
ggdotplot(), ggstripchart(),
gghistogram(), ggdensity(),
ggecdf() and ggqqplot() can now handle one
single numeric vector.# Example
ggboxplot(iris$Sepal.Length)gghistogram(), when add_density = TRUE, y scale
remains = “..count..”.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.