NEWS.md
ggadjust_pvalue() added to adjust p-values produced by geom_pwc() on a ggplot (#522).gene_expression
ggpubr.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/228
ggpubr requires now a version of cowplot >= 1.1.1
ggtexttable(): 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():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, #77
bracket.size added to stat_compare_means() @mtmatter, #43
stat_cor() supports R^2 as an option @philament, #32
position added in gghistogram(). Allowed values include “identity”, “stack”, “dodge”.ci added in ggerrorplot() @abrar-alshaer, #94
ggscatter() 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, #1
ggtext() 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..”.