ggpubr Files

New features

• New function ggadjust_pvalue() added to adjust p-values produced by geom_pwc() on a ggplot (#522).
• New data added: gene_expression
• Global options: New available package options: 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).

Major changes

• 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

Minor changes

• 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 [#158]
• ggarrange(): using null_device to avoid blank page [#306] and [#158]
• Indexing variable in a data frame: using df[[x]] instead of df[, x] to make sure that the result is a vector even if the df is a tibble.
• ggexport(): support added for graphics device svg (#469)
• ggpie() and ggdonutchart() now fully reacts to the option lab.font (#502)
• Replacing deprecated 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.
• Enable faceting by column names with spaces (#391)
• Licence changed to GPL (>= 2) (#482)
• desc_statby() doc updated to clarify the difference between SD (standard deviation) and SE (standard error) (#492)
• The message geom_smooth() using formula 'y ~ x' is now turned off in <inline_block>1</inline_block>(#488

Bug fixes

• 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)
• Requiring 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)