ggpubr Files

New features

• New functions added to customize 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).
• ggpubr functions updated to handle non-standard column names, for example ("A-A") (#229).
• New function create_aes() added to create aes mapping from a list. Makes programming easy with ggplot2 (#229).
• New argument 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.
• New errorbar functions - 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.
• New function 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]).

Major changes

• The following enhancement has been added to ggscatterhist() (@juliechevalier, [#176]):
  • the output of 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 verbs
  • An S3 printing method is now available for an object of class ggscatterhist. The printing method displays the arranged final figure.

Minor changes

• Now, when creating a box plot with error bars, color and fill argiments are taken into account in the errorbar function (#105).
• New argument alternative supported in stat_cor() (#276).
• New argument position in ggline() to make position "dodged" (#52).
• New argument outlier.shape in ggboxplot(). Default is 19. To hide outlier, specify outlier.shape = NA. When jitter is added, then outliers will be automatically hidden.
• Sorting can be now disabled in ggdotchart() using the option sorting = "none" (#115, [#223]).
• New argument weight added in gghistogram() for creating a weighted histogram (#215)
• Now 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])
• New argument bracket.shorten added in stat_pvalue_manual() and geom_bracket(). a small numeric value in [0-1] for shortening the with of bracket (#285).
• New argument 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).
• New argument numeric.x.axis added in ggerrorplot(); logical value, If TRUE, x axis will be treated as numeric. Default is FALSE (#280).
• The option width is now considered in ggadd() for plotting error bars (#278).
• New argument linetype in ggpaired().
• geom_exec() used in ggpaired() to add lines between paired points.
• ggmaplot() now supports two input formats (#198):
  1. baseMean | log2FoldChange|padj: Here, we'll use log2(baseMean) as the x-axis variable
  2. baseMeanLog2 | log2FoldChange|padj: here, baseMeanLog2 is assumed to be the mean of logged values; so we'll use it as x-axis variable without any transformation.
• new arguments added in ggmaplot():
  • alpha for controlling point transparency/density (@apcamargo, #152).
  • label.select to select specific genes to show on the plot (@apastore, #70)
• In ggadd() the fill argument is considered for jitter points only when the point shape is in 21:25 (@atakanekiz, [#148]).
• New argument parse added in ggscatter() and in ggtext(). If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath (#250).
• New argument stroke supported in ggscatter() and in ggline(). Used only for shapes 21-24 to control the thickness of points border (@bioguy2018, [#258]).
• the 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).

Bug fixes

• 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).
• the argument 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]).
• Now, gghistogram() supports the paramter yticks.by (@Chitanda-Satou, [#258]).