├── .Rbuildignore ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ └── issue_template.md └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── DESCRIPTION ├── ISSUE_TEMPLATE.md ├── NAMESPACE ├── NEWS.md ├── R ├── add_summary.R ├── annotate_figure.R ├── as_ggplot.R ├── as_npc.R ├── axis_scale.R ├── background_image.R ├── bgcolor.R ├── border.R ├── compare_means.R ├── create_aes.R ├── desc_statby.R ├── diff_express.R ├── facet.R ├── font.R ├── gene_citation.R ├── gene_expression.R ├── geom_bracket.R ├── geom_exec.R ├── geom_pwc.R ├── get_breaks.R ├── get_coord.R ├── get_legend.R ├── get_palette.R ├── ggadd.R ├── ggadjust_pvalue.R ├── ggarrange.R ├── ggballoonplot.R ├── ggbarplot.R ├── ggboxplot.R ├── ggdensity.R ├── ggdonutchart.R ├── ggdotchart.R ├── ggdotplot.R ├── ggecdf.R ├── ggerrorplot.R ├── ggexport.R ├── gghistogram.R ├── ggline.R ├── ggmaplot.R ├── ggpaired.R ├── ggpar.R ├── ggparagraph.R ├── ggpie.R ├── ggpubr-package.R ├── ggpubr_args.R ├── ggpubr_options.R ├── ggqqplot.R ├── ggscatter.R ├── ggscatterhist.R ├── ggstripchart.R ├── ggsummarystats.R ├── ggtext.R ├── ggtexttable.R ├── ggviolin.R ├── gradient_color.R ├── grids.R ├── npc_to_data_coord.R ├── reexports.R ├── rotate.R ├── rotate_axis_text.R ├── rremove.R ├── set_palette.R ├── show_line_types.R ├── show_point_shapes.R ├── stat_anova_test.R ├── stat_central_tendency.R ├── stat_chull.R ├── stat_compare_means.R ├── stat_conf_ellipse.R ├── stat_cor.R ├── stat_friedman_test.R ├── stat_kruskal_test.R ├── stat_mean.R ├── stat_overlay_normal_density.R ├── stat_pvalue_manual.R ├── stat_regline_equation.R ├── stat_stars.R ├── stat_welch_anova_test.R ├── text_grob.R ├── theme_pubr.R ├── theme_transparent.R ├── utilities.R ├── utilities_base.R ├── utilities_color.R ├── utilities_label.R ├── utils-aes.R ├── utils-geom-signif.R ├── utils-pipe.R ├── utils-tidyr.R └── utils_stat_test_label.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── cran-comments.md ├── data-raw └── gene_expression.R ├── data ├── diff_express.rda ├── gene_citation.rda └── gene_expression.rda ├── docs ├── 404.html ├── ISSUE_TEMPLATE.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── docsearch.json ├── extra.js ├── favicon.ico ├── files │ ├── ggtexttable-theme.pdf │ ├── ggtexttable-theme.pptx │ └── ggtexttable-theme.xlsx ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── Rplot004.png │ ├── Rplot005.png │ ├── Rplot006.png │ ├── Rplot007.png │ ├── Rplot008.png │ ├── Rplot009.png │ ├── Rplot010.png │ ├── Rplot011.png │ ├── Rplot012.png │ ├── Rplot013.png │ ├── Rplot014.png │ ├── Rplot015.png │ ├── Rplot016.png │ ├── Rplot017.png │ ├── add_summary-1 2.png │ ├── add_summary-1.png │ ├── add_summary-2.png │ ├── add_summary.html │ ├── annotate_figure-1.png │ ├── annotate_figure.html │ ├── as_ggplot-1.png │ ├── as_ggplot.html │ ├── as_npc.html │ ├── axis_scale-1.png │ ├── axis_scale-2.png │ ├── axis_scale.html │ ├── background_image.html │ ├── bgcolor-1.png │ ├── bgcolor-2.png │ ├── bgcolor.html │ ├── border-1.png │ ├── border-2.png │ ├── border.html │ ├── compare_means.html │ ├── create_aes-1.png │ ├── create_aes.html │ ├── desc_statby.html │ ├── diff_express-1.png │ ├── diff_express-2 2.png │ ├── diff_express-2.png │ ├── diff_express.html │ ├── facet-1 2.png │ ├── facet-1.png │ ├── facet-2.png │ ├── facet-3.png │ ├── facet.html │ ├── font-1 2.png │ ├── font-1.png │ ├── font-2.png │ ├── font-3.png │ ├── font.html │ ├── gene_citation-1.png │ ├── gene_citation.html │ ├── gene_expression-1.png │ ├── gene_expression.html │ ├── geom_bracket-1.png │ ├── geom_bracket-2.png │ ├── geom_bracket-3.png │ ├── geom_bracket-4.png │ ├── geom_bracket-5.png │ ├── geom_bracket-6.png │ ├── geom_bracket-7.png │ ├── geom_bracket.html │ ├── geom_exec.html │ ├── geom_pwc-1.png │ ├── geom_pwc-2.png │ ├── geom_pwc-3.png │ ├── geom_pwc-4.png │ ├── geom_pwc-5.png │ ├── geom_pwc.html │ ├── geom_signif.html │ ├── get_breaks-1.png │ ├── get_breaks-2.png │ ├── get_breaks-3.png │ ├── get_breaks.html │ ├── get_coord.html │ ├── get_legend-1.png │ ├── get_legend-2.png │ ├── get_legend.html │ ├── get_palette-1.png │ ├── get_palette-2.png │ ├── get_palette-3.png │ ├── get_palette-4.png │ ├── get_palette-5.png │ ├── get_palette-6.png │ ├── get_palette.html │ ├── ggadd-1.png │ ├── ggadd-2.png │ ├── ggadd.html │ ├── ggadjust_pvalue-1.png │ ├── ggadjust_pvalue-2.png │ ├── ggadjust_pvalue-3.png │ ├── ggadjust_pvalue-4.png │ ├── ggadjust_pvalue.html │ ├── ggarrange-1 2.png │ ├── ggarrange-1.png │ ├── ggarrange-2.png │ ├── ggarrange.html │ ├── ggballoonplot-1.png │ ├── ggballoonplot-2.png │ ├── ggballoonplot-3.png │ ├── ggballoonplot-4.png │ ├── ggballoonplot-5.png │ ├── ggballoonplot-6.png │ ├── ggballoonplot-7.png │ ├── ggballoonplot-8.png │ ├── ggballoonplot.html │ ├── ggbarplot-1 2.png │ ├── ggbarplot-1.png │ ├── ggbarplot-10.png │ ├── ggbarplot-11.png │ ├── ggbarplot-12.png │ ├── ggbarplot-13.png │ ├── ggbarplot-14.png │ ├── ggbarplot-15.png │ ├── ggbarplot-16.png │ ├── ggbarplot-17.png │ ├── ggbarplot-2.png │ ├── ggbarplot-3.png │ ├── ggbarplot-4.png │ ├── ggbarplot-5.png │ ├── ggbarplot-6.png │ ├── ggbarplot-7.png │ ├── ggbarplot-8.png │ ├── ggbarplot-9.png │ ├── ggbarplot.html │ ├── ggboxplot-1.png │ ├── ggboxplot-10.png │ ├── ggboxplot-11.png │ ├── ggboxplot-2.png │ ├── ggboxplot-3.png │ ├── ggboxplot-4.png │ ├── ggboxplot-5.png │ ├── ggboxplot-6.png │ ├── ggboxplot-7.png │ ├── ggboxplot-8.png │ ├── ggboxplot-9.png │ ├── ggboxplot.html │ ├── ggdensity-1.png │ ├── ggdensity-2.png │ ├── ggdensity-3.png │ ├── ggdensity.html │ ├── ggdonutchart-1.png │ ├── ggdonutchart-2.png │ ├── ggdonutchart-3.png │ ├── ggdonutchart-4.png │ ├── ggdonutchart.html │ ├── ggdotchart-1 2.png │ ├── ggdotchart-1.png │ ├── ggdotchart-2.png │ ├── ggdotchart-3.png │ ├── ggdotchart.html │ ├── ggdotplot-1 2.png │ ├── ggdotplot-1.png │ ├── ggdotplot-2.png │ ├── ggdotplot-3.png │ ├── ggdotplot-4.png │ ├── ggdotplot-5.png │ ├── ggdotplot-6.png │ ├── ggdotplot.html │ ├── ggecdf-1.png │ ├── ggecdf-2.png │ ├── ggecdf.html │ ├── ggerrorplot-1 2.png │ ├── ggerrorplot-1.png │ ├── ggerrorplot-2.png │ ├── ggerrorplot-3.png │ ├── ggerrorplot-4.png │ ├── ggerrorplot-5.png │ ├── ggerrorplot-6.png │ ├── ggerrorplot-7.png │ ├── ggerrorplot-8.png │ ├── ggerrorplot.html │ ├── ggexport.html │ ├── gghistogram-1.png │ ├── gghistogram-2.png │ ├── gghistogram-3.png │ ├── gghistogram-4.png │ ├── gghistogram-5.png │ ├── gghistogram.html │ ├── ggline-1 2.png │ ├── ggline-1.png │ ├── ggline-10.png │ ├── ggline-11.png │ ├── ggline-12.png │ ├── ggline-13.png │ ├── ggline-2.png │ ├── ggline-3.png │ ├── ggline-4.png │ ├── ggline-5.png │ ├── ggline-6.png │ ├── ggline-7.png │ ├── ggline-8.png │ ├── ggline-9.png │ ├── ggline.html │ ├── ggmaplot-1 2.png │ ├── ggmaplot-1.png │ ├── ggmaplot-2.png │ ├── ggmaplot-3 2.png │ ├── ggmaplot-3.png │ ├── ggmaplot.html │ ├── ggpaired-1.png │ ├── ggpaired-2.png │ ├── ggpaired.html │ ├── ggpar-1.png │ ├── ggpar-10.png │ ├── ggpar-11.png │ ├── ggpar-12.png │ ├── ggpar-13.png │ ├── ggpar-14.png │ ├── ggpar-15.png │ ├── ggpar-2.png │ ├── ggpar-3.png │ ├── ggpar-4.png │ ├── ggpar-5.png │ ├── ggpar-6.png │ ├── ggpar-7.png │ ├── ggpar-8.png │ ├── ggpar-9.png │ ├── ggpar.html │ ├── ggparagraph-1 2.png │ ├── ggparagraph-1.png │ ├── ggparagraph.html │ ├── ggpie-1.png │ ├── ggpie-2.png │ ├── ggpie-3.png │ ├── ggpie-4.png │ ├── ggpie-5.png │ ├── ggpie.html │ ├── ggpubr-package.html │ ├── ggpubr_args.html │ ├── ggpubr_options.html │ ├── ggqqplot-1.png │ ├── ggqqplot-2.png │ ├── ggqqplot.html │ ├── ggscatter-1 2.png │ ├── ggscatter-1.png │ ├── ggscatter-2.png │ ├── ggscatter-3.png │ ├── ggscatter-4.png │ ├── ggscatter-5.png │ ├── ggscatter-6.png │ ├── ggscatter.html │ ├── ggscatterhist-1 2.png │ ├── ggscatterhist-1.png │ ├── ggscatterhist-2.png │ ├── ggscatterhist-3.png │ ├── ggscatterhist-4.png │ ├── ggscatterhist.html │ ├── ggstripchart-1 2.png │ ├── ggstripchart-1.png │ ├── ggstripchart-2.png │ ├── ggstripchart-3.png │ ├── ggstripchart-4.png │ ├── ggstripchart-5.png │ ├── ggstripchart-6.png │ ├── ggstripchart-7.png │ ├── ggstripchart-8.png │ ├── ggstripchart-9.png │ ├── ggstripchart.html │ ├── ggsummarystats-1.png │ ├── ggsummarystats-2.png │ ├── ggsummarystats-3.png │ ├── ggsummarystats-4.png │ ├── ggsummarystats-5.png │ ├── ggsummarystats-6.png │ ├── ggsummarystats-7.png │ ├── ggsummarystats.html │ ├── ggtext-1 2.png │ ├── ggtext-1.png │ ├── ggtext-2 2.png │ ├── ggtext-2.png │ ├── ggtext.html │ ├── ggtexttable-1.png │ ├── ggtexttable-10.png │ ├── ggtexttable-11.png │ ├── ggtexttable-12.png │ ├── ggtexttable-13.png │ ├── ggtexttable-14.png │ ├── ggtexttable-15.png │ ├── ggtexttable-16.png │ ├── ggtexttable-17.png │ ├── ggtexttable-2.png │ ├── ggtexttable-3.png │ ├── ggtexttable-4.png │ ├── ggtexttable-5.png │ ├── ggtexttable-6.png │ ├── ggtexttable-7.png │ ├── ggtexttable-8.png │ ├── ggtexttable-9.png │ ├── ggtexttable.html │ ├── ggviolin-1.png │ ├── ggviolin-10.png │ ├── ggviolin-11.png │ ├── ggviolin-12.png │ ├── ggviolin-2.png │ ├── ggviolin-3.png │ ├── ggviolin-4.png │ ├── ggviolin-5.png │ ├── ggviolin-6.png │ ├── ggviolin-7.png │ ├── ggviolin-8.png │ ├── ggviolin-9.png │ ├── ggviolin.html │ ├── gradient_color-1.png │ ├── gradient_color-2.png │ ├── gradient_color-3.png │ ├── gradient_color-4.png │ ├── gradient_color-5.png │ ├── gradient_color.html │ ├── grids-1.png │ ├── grids-2.png │ ├── grids.html │ ├── index.html │ ├── npc_to_data_coord.html │ ├── pipe.html │ ├── reexports.html │ ├── rotate-1.png │ ├── rotate-2.png │ ├── rotate.html │ ├── rotate_axis_text-1.png │ ├── rotate_axis_text-2.png │ ├── rotate_axis_text-3.png │ ├── rotate_axis_text-4.png │ ├── rotate_axis_text.html │ ├── rremove-1.png │ ├── rremove-2.png │ ├── rremove-3 2.png │ ├── rremove-3.png │ ├── rremove.html │ ├── set_palette-1.png │ ├── set_palette-2.png │ ├── set_palette.html │ ├── show_line_types-1.png │ ├── show_line_types.html │ ├── show_point_shapes-1.png │ ├── show_point_shapes.html │ ├── stat_anova_test-1.png │ ├── stat_anova_test-2.png │ ├── stat_anova_test-3.png │ ├── stat_anova_test-4.png │ ├── stat_anova_test-5.png │ ├── stat_anova_test-6.png │ ├── stat_anova_test-7.png │ ├── stat_anova_test-8.png │ ├── stat_anova_test.html │ ├── stat_central_tendency-1.png │ ├── stat_central_tendency-2.png │ ├── stat_central_tendency-3.png │ ├── stat_central_tendency-4.png │ ├── stat_central_tendency.html │ ├── stat_chull-1.png │ ├── stat_chull-2.png │ ├── stat_chull.html │ ├── stat_compare_means-1.png │ ├── stat_compare_means-2.png │ ├── stat_compare_means-3.png │ ├── stat_compare_means-4.png │ ├── stat_compare_means-5.png │ ├── stat_compare_means-6.png │ ├── stat_compare_means.html │ ├── stat_conf_ellipse-1.png │ ├── stat_conf_ellipse-2.png │ ├── stat_conf_ellipse.html │ ├── stat_cor-1 2.png │ ├── stat_cor-1.png │ ├── stat_cor-2.png │ ├── stat_cor-3.png │ ├── stat_cor-4.png │ ├── stat_cor-5.png │ ├── stat_cor.html │ ├── stat_friedman_test-1 2.png │ ├── stat_friedman_test-1.png │ ├── stat_friedman_test-2.png │ ├── stat_friedman_test-3.png │ ├── stat_friedman_test-4.png │ ├── stat_friedman_test-5.png │ ├── stat_friedman_test-6.png │ ├── stat_friedman_test-7.png │ ├── stat_friedman_test.html │ ├── stat_kruskal_test-1.png │ ├── stat_kruskal_test-2.png │ ├── stat_kruskal_test-3.png │ ├── stat_kruskal_test-4.png │ ├── stat_kruskal_test-5.png │ ├── stat_kruskal_test-6.png │ ├── stat_kruskal_test-7.png │ ├── stat_kruskal_test.html │ ├── stat_mean-1.png │ ├── stat_mean.html │ ├── stat_overlay_normal_density-1.png │ ├── stat_overlay_normal_density-2.png │ ├── stat_overlay_normal_density-3.png │ ├── stat_overlay_normal_density.html │ ├── stat_pvalue_manual-1.png │ ├── stat_pvalue_manual-2.png │ ├── stat_pvalue_manual-3.png │ ├── stat_pvalue_manual-4.png │ ├── stat_pvalue_manual.html │ ├── stat_regline_equation-1 2.png │ ├── stat_regline_equation-1.png │ ├── stat_regline_equation-2.png │ ├── stat_regline_equation-3.png │ ├── stat_regline_equation.html │ ├── stat_stars-1.png │ ├── stat_stars.html │ ├── stat_welch_anova_test-1 2.png │ ├── stat_welch_anova_test-1.png │ ├── stat_welch_anova_test-2.png │ ├── stat_welch_anova_test-3.png │ ├── stat_welch_anova_test-4.png │ ├── stat_welch_anova_test-5.png │ ├── stat_welch_anova_test-6.png │ ├── stat_welch_anova_test-7.png │ ├── stat_welch_anova_test.html │ ├── text_grob-1.png │ ├── text_grob.html │ ├── theme_pubr-1 2.png │ ├── theme_pubr-1.png │ ├── theme_pubr-2.png │ ├── theme_pubr-3.png │ ├── theme_pubr.html │ ├── theme_transparent-1.png │ ├── theme_transparent-2.png │ └── theme_transparent.html ├── sitemap.xml └── tools │ ├── README-cleveland-dot-plots-1.png │ ├── README-deviation-graphs-1.png │ ├── README-deviation-graphs-horizontal-1.png │ ├── README-ggpubr-1.png │ ├── README-ggpubr-2.png │ ├── README-ggpubr-box-plot-dot-plots-strip-charts-1.png │ ├── README-ggpubr-box-plot-dot-plots-strip-charts-2.png │ ├── README-ggpubr-box-plot-dot-plots-strip-charts-3.png │ ├── README-lollipop-chart-1.png │ ├── README-lollipop-chart-deviation-1.png │ ├── README-lollipop-chart-rotate-1.png │ ├── README-ordered-bar-plots-1.png │ └── README-ordered-bar-plots-by-groups-1.png ├── ggpubr.Rproj ├── images ├── adjusted-p-value-box-plot-faceted.jpeg └── adjusted-p-values-faceted-boxplots-formatted.jpeg ├── inst ├── demo-data │ └── housetasks.txt └── images │ └── background-image.png ├── man ├── add_summary.Rd ├── annotate_figure.Rd ├── as_ggplot.Rd ├── as_npc.Rd ├── axis_scale.Rd ├── background_image.Rd ├── bgcolor.Rd ├── border.Rd ├── compare_means.Rd ├── create_aes.Rd ├── desc_statby.Rd ├── diff_express.Rd ├── facet.Rd ├── font.Rd ├── gene_citation.Rd ├── gene_expression.Rd ├── geom_bracket.Rd ├── geom_exec.Rd ├── geom_pwc.Rd ├── geom_signif.Rd ├── get_breaks.Rd ├── get_coord.Rd ├── get_legend.Rd ├── get_palette.Rd ├── ggadd.Rd ├── ggadjust_pvalue.Rd ├── ggarrange.Rd ├── ggballoonplot.Rd ├── ggbarplot.Rd ├── ggboxplot.Rd ├── ggdensity.Rd ├── ggdonutchart.Rd ├── ggdotchart.Rd ├── ggdotplot.Rd ├── ggecdf.Rd ├── ggerrorplot.Rd ├── ggexport.Rd ├── gghistogram.Rd ├── ggline.Rd ├── ggmaplot.Rd ├── ggpaired.Rd ├── ggpar.Rd ├── ggparagraph.Rd ├── ggpie.Rd ├── ggpubr-package.Rd ├── ggpubr_args.Rd ├── ggpubr_options.Rd ├── ggqqplot.Rd ├── ggscatter.Rd ├── ggscatterhist.Rd ├── ggstripchart.Rd ├── ggsummarystats.Rd ├── ggtext.Rd ├── ggtexttable.Rd ├── ggviolin.Rd ├── gradient_color.Rd ├── grids.Rd ├── npc_to_data_coord.Rd ├── pipe.Rd ├── reexports.Rd ├── rotate.Rd ├── rotate_axis_text.Rd ├── rremove.Rd ├── set_palette.Rd ├── show_line_types.Rd ├── show_point_shapes.Rd ├── stat_anova_test.Rd ├── stat_central_tendency.Rd ├── stat_chull.Rd ├── stat_compare_means.Rd ├── stat_conf_ellipse.Rd ├── stat_cor.Rd ├── stat_friedman_test.Rd ├── stat_kruskal_test.Rd ├── stat_mean.Rd ├── stat_overlay_normal_density.Rd ├── stat_pvalue_manual.Rd ├── stat_regline_equation.Rd ├── stat_stars.Rd ├── stat_welch_anova_test.Rd ├── text_grob.Rd ├── theme_pubr.Rd └── theme_transparent.Rd ├── pkgdown └── extra.js ├── tests ├── testthat.R └── testthat │ ├── test-add_stat_label.R │ ├── test-as_npc.R │ ├── test-check_data.R │ ├── test-compare_means.R │ ├── test-create_aes.R │ ├── test-facet.R │ ├── test-geom_pwc.R │ ├── test-get_coord.R │ ├── test-ggadjust_pvalue.R │ ├── test-ggboxplot.R │ ├── test-gghistogram.R │ ├── test-ggscatter.R │ ├── test-ggstripchart.R │ ├── test-ggtext.R │ ├── test-stat_anova_test.R │ ├── test-stat_compare_means.R │ ├── test-stat_friedman_test.R │ ├── test-stat_kruskal_test.R │ ├── test-stat_welch_anova_test.R │ └── test-utils-tidyr.R └── tools ├── README-cleveland-dot-plots-1.png ├── README-deviation-graphs-1.png ├── README-deviation-graphs-horizontal-1.png ├── README-ggpubr-1.png ├── README-ggpubr-2.png ├── README-ggpubr-box-plot-dot-plots-strip-charts-1.png ├── README-ggpubr-box-plot-dot-plots-strip-charts-2.png ├── README-ggpubr-box-plot-dot-plots-strip-charts-3.png ├── README-lollipop-chart-1.png ├── README-lollipop-chart-deviation-1.png ├── README-lollipop-chart-rotate-1.png ├── README-ordered-bar-plots-1.png └── README-ordered-bar-plots-by-groups-1.png /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^pkgdown$ 2 | ^pkgdown/* 3 | ^CRAN-RELEASE$ 4 | ^.*\.Rproj$ 5 | ^\.Rproj\.user$ 6 | ^README\.Rmd$ 7 | ^README-.*\.png$ 8 | ^cran-comments\.md$ 9 | ^docs$ 10 | ^images$ 11 | ^_pkgdown\.yml$ 12 | ^TODO\.Rmd$ 13 | ^\.github$ 14 | ^data-raw$ 15 | ^ISSUE_TEMPLATE\.md$ 16 | -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/issue_template.md: -------------------------------------------------------------------------------- 1 | Please briefly describe your problem and what output you expect. 2 | 3 | Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading . 4 | 5 | Delete these instructions once you have read them. 6 | 7 | --- 8 | 9 | Brief description of the problem 10 | 11 | ```r 12 | # insert reprex here 13 | ``` 14 | -------------------------------------------------------------------------------- /.github/workflows/R-CMD-check.yaml: -------------------------------------------------------------------------------- 1 | # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples 2 | # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help 3 | on: 4 | push: 5 | branches: [main, master] 6 | pull_request: 7 | branches: [main, master] 8 | 9 | name: R-CMD-check 10 | 11 | jobs: 12 | R-CMD-check: 13 | runs-on: ${{ matrix.config.os }} 14 | 15 | name: ${{ matrix.config.os }} (${{ matrix.config.r }}) 16 | 17 | strategy: 18 | fail-fast: false 19 | matrix: 20 | config: 21 | - {os: macos-latest, r: 'release'} 22 | - {os: windows-latest, r: 'release'} 23 | - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} 24 | - {os: ubuntu-latest, r: 'release'} 25 | - {os: ubuntu-latest, r: 'oldrel-1'} 26 | 27 | env: 28 | GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} 29 | R_KEEP_PKG_SOURCE: yes 30 | 31 | steps: 32 | - uses: actions/checkout@v3 33 | 34 | - uses: r-lib/actions/setup-pandoc@v2 35 | 36 | - uses: r-lib/actions/setup-r@v2 37 | with: 38 | r-version: ${{ matrix.config.r }} 39 | http-user-agent: ${{ matrix.config.http-user-agent }} 40 | use-public-rspm: true 41 | 42 | - uses: r-lib/actions/setup-r-dependencies@v2 43 | with: 44 | extra-packages: any::rcmdcheck 45 | needs: check 46 | 47 | - uses: r-lib/actions/check-r-package@v2 48 | with: 49 | upload-snapshots: true 50 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .DS_Store 5 | docs/.DS_Store 6 | TODO.Rmd 7 | -------------------------------------------------------------------------------- /ISSUE_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | Please briefly describe your problem and what output you expect. 2 | 3 | Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading . 4 | 5 | Delete these instructions once you have read them. 6 | 7 | --- 8 | 9 | ### Expected behavior 10 | 11 | ### Actual behavior 12 | 13 | ### Steps to reproduce the problem 14 | 15 | ```r 16 | # insert reprex here 17 | ``` 18 | 19 | 20 | ### `session_info()` 21 | 22 | ````r 23 | # please paste here the result of 24 | devtools::session_info() 25 | ```` 26 | -------------------------------------------------------------------------------- /R/as_ggplot.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R 2 | NULL 3 | #'Storing grid.arrange() arrangeGrob() and plots 4 | #' 5 | #'@description Transform the output of 6 | #' \code{\link[gridExtra:arrangeGrob]{arrangeGrob}()} and 7 | #' \code{\link[gridExtra:arrangeGrob]{grid.arrange}()} to a an object of class 8 | #' ggplot. 9 | #'@param x an object of class gtable or grob as returned by the functions 10 | #' \code{\link[gridExtra:arrangeGrob]{arrangeGrob}()} and 11 | #' \code{\link[gridExtra:arrangeGrob]{grid.arrange}()}. 12 | #'@return an object of class ggplot. 13 | #' 14 | #' @examples 15 | #' # Creat some plots 16 | #'bxp <- ggboxplot(iris, x = "Species", y = "Sepal.Length") 17 | #'vp <- ggviolin(iris, x = "Species", y = "Sepal.Length", 18 | #' add = "mean_sd") 19 | #' 20 | #'# Arrange the plots in one page 21 | #'# Returns a gtable (grob) object 22 | #'library(gridExtra) 23 | #'gt <- arrangeGrob(bxp, vp, ncol = 2) 24 | #' 25 | #'# Transform to a ggplot and print 26 | #'as_ggplot(gt) 27 | #' 28 | #'@export 29 | as_ggplot <- function(x){ 30 | 31 | # Open null device to avoid blank page before plot------ 32 | # see cowplot:::as_grob.ggplot 33 | null_device <- base::getOption( 34 | "ggpubr.null_device", 35 | default = cowplot::pdf_null_device 36 | ) 37 | cur_dev <- grDevices::dev.cur() 38 | # Open null device to avoid blank page before plot 39 | null_device(width = 6, height = 6) 40 | null_dev <- grDevices::dev.cur() 41 | on.exit({ 42 | grDevices::dev.off(null_dev) 43 | if (cur_dev > 1) grDevices::dev.set(cur_dev) 44 | }) 45 | 46 | # Convert to ggplot------------- 47 | cowplot::ggdraw() + 48 | cowplot::draw_grob(grid::grobTree(x)) 49 | } 50 | -------------------------------------------------------------------------------- /R/background_image.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R 2 | NULL 3 | #'Add Background Image to ggplot2 4 | #'@description Add background image to ggplot2. 5 | #'@param raster.img raster object to display, as returned by the function 6 | #' \code{readPNG()}[in \code{png} package] and \code{readJPEG()} [in \code{jpeg} package]. 7 | #'@author Alboukadel Kassambara 8 | #' @examples 9 | #' \dontrun{ 10 | #'install.packages("png") 11 | #' 12 | #'# Import the image 13 | #'img.file <- system.file(file.path("images", "background-image.png"), 14 | #' package = "ggpubr") 15 | #'img <- png::readPNG(img.file) 16 | #' 17 | #'# Plot with background image 18 | #'ggplot(iris, aes(Species, Sepal.Length))+ 19 | #' background_image(img)+ 20 | #' geom_boxplot(aes(fill = Species), color = "white")+ 21 | #' fill_palette("jco") 22 | #' } 23 | #' 24 | #'@export 25 | background_image <- function(raster.img){ 26 | annotation_raster(raster.img, 27 | xmin = -Inf, xmax = Inf, 28 | ymin = -Inf, ymax = Inf) 29 | } 30 | -------------------------------------------------------------------------------- /R/bgcolor.R: -------------------------------------------------------------------------------- 1 | #'Change ggplot Panel Background Color 2 | #' 3 | #' @description Change ggplot panel background color. 4 | #' @param color background color. 5 | #' 6 | #' @seealso \link{border}(). 7 | #' 8 | #'@examples 9 | #'# Load data 10 | #'data("ToothGrowth") 11 | #'df <- ToothGrowth 12 | #' 13 | #'# Basic plot 14 | #'p <- ggboxplot(df, x = "dose", y = "len") 15 | #'p 16 | #' 17 | #'# Change panel background color 18 | #' p + 19 | #' bgcolor("#BFD5E3")+ 20 | #' border("#BFD5E3") 21 | #'@export 22 | bgcolor <- function(color){ 23 | theme(panel.background = element_rect(fill = color)) 24 | } 25 | -------------------------------------------------------------------------------- /R/border.R: -------------------------------------------------------------------------------- 1 | #'Set ggplot Panel Border Line 2 | #' 3 | #'@description Change or set ggplot panel border. 4 | #'@param color border line color. 5 | #'@param size numeric value specifying border line size. 6 | #'@param linetype line type. An integer (0:8), a name (blank, solid, dashed, 7 | #' dotted, dotdash, longdash, twodash). Sess \code{\link{show_line_types}}. 8 | #' 9 | #' 10 | #'@examples 11 | #'# Load data 12 | #'data("ToothGrowth") 13 | #'df <- ToothGrowth 14 | #' 15 | #'# Basic plot 16 | #'p <- ggboxplot(df, x = "dose", y = "len") 17 | #'p 18 | #' 19 | #'# Add border 20 | #' p + border() 21 | #'@export 22 | border <- function(color = "black", size = 0.8, linetype = NULL){ 23 | theme(panel.background = element_rect(color = color, size = size, linetype = linetype), 24 | axis.line = element_blank()) 25 | } 26 | -------------------------------------------------------------------------------- /R/diff_express.R: -------------------------------------------------------------------------------- 1 | #' Differential gene expression analysis results 2 | #' 3 | #' @description Differential gene expression analysis results obtained from 4 | #' comparing the RNAseq data of two different cell populations using DESeq2 5 | #' @name diff_express 6 | #' @docType data 7 | #' @usage data("diff_express") 8 | #' @format A data frame with 36028 rows and 5 columns. \describe{ 9 | #' \item{\code{name}}{gene names} \item{\code{baseMean}}{mean expression 10 | #' signal across all samples} \item{\code{log2FoldChange}}{log2 fold change} 11 | #' \item{\code{padj}}{Adjusted p-value}\item{\code{detection_call}}{a numeric 12 | #' vector specifying whether the genes is expressed (value = 1) or not (value = 0).}} 13 | #' 14 | #' @examples 15 | #' data(diff_express) 16 | #' 17 | #' # Default plot 18 | #'ggmaplot(diff_express, main = expression("Group 1" %->% "Group 2"), 19 | #' fdr = 0.05, fc = 2, size = 0.4, 20 | #' palette = c("#B31B21", "#1465AC", "darkgray"), 21 | #' genenames = as.vector(diff_express$name), 22 | #' legend = "top", top = 20, 23 | #' font.label = c("bold", 11), 24 | #' font.legend = "bold", 25 | #' font.main = "bold", 26 | #' ggtheme = ggplot2::theme_minimal()) 27 | #' 28 | #' # Add rectangle around labesl 29 | #'ggmaplot(diff_express, main = expression("Group 1" %->% "Group 2"), 30 | #' fdr = 0.05, fc = 2, size = 0.4, 31 | #' palette = c("#B31B21", "#1465AC", "darkgray"), 32 | #' genenames = as.vector(diff_express$name), 33 | #' legend = "top", top = 20, 34 | #' font.label = c("bold", 11), label.rectangle = TRUE, 35 | #' font.legend = "bold", 36 | #' font.main = "bold", 37 | #' ggtheme = ggplot2::theme_minimal()) 38 | #' 39 | NULL 40 | -------------------------------------------------------------------------------- /R/gene_citation.R: -------------------------------------------------------------------------------- 1 | #'Gene Citation Index 2 | #' 3 | #'@description Contains the mean citation index of 66 genes obtained by 4 | #' assessing PubMed abstracts and annotations using two key words i) Gene name 5 | #' + b cell differentiation and ii) Gene name + plasma cell differentiation. 6 | #'@name gene_citation 7 | #'@docType data 8 | #'@usage data("gene_citation") 9 | #'@format A data frame with 66 rows and 2 columns. \describe{ 10 | #' \item{\code{gene}}{gene names} \item{\code{citation_index}}{mean citation index} } 11 | #' 12 | #' @examples 13 | #' data(gene_citation) 14 | #' 15 | #'# Some key genes of interest to be highlighted 16 | #'key.gns <- c("MYC", "PRDM1", "CD69", "IRF4", "CASP3", "BCL2L1", "MYB", "BACH2", "BIM1", "PTEN", 17 | #' "KRAS", "FOXP1", "IGF1R", "KLF4", "CDK6", "CCND2", "IGF1", "TNFAIP3", "SMAD3", "SMAD7", 18 | #' "BMPR2", "RB1", "IGF2R", "ARNT") 19 | #'# Density distribution 20 | #'ggdensity(gene_citation, x = "citation_index", y = "..count..", 21 | #' xlab = "Number of citation", 22 | #' ylab = "Number of genes", 23 | #' fill = "lightgray", color = "black", 24 | #' label = "gene", label.select = key.gns, repel = TRUE, 25 | #' font.label = list(color= "citation_index"), 26 | #' xticks.by = 20, # Break x ticks by 20 27 | #' gradient.cols = c("blue", "red"), 28 | #' legend = "bottom", 29 | #' legend.title = "" # Hide legend title 30 | #' ) 31 | #' 32 | NULL 33 | -------------------------------------------------------------------------------- /R/gene_expression.R: -------------------------------------------------------------------------------- 1 | #'Gene Expression Data 2 | #' 3 | #'@description Gene expression data extracted from TCGA using the `RTCGA` and 4 | #' `RTCGA.mRNA` R packages. It contains the mRNA expression for 3 genes - 5 | #' GATA3, PTEN and XBP1- from 3 different datasets: Breast invasive carcinoma 6 | #' (BRCA), Ovarian serous cystadenocarcinoma (OV) and Lung squamous cell 7 | #' carcinoma (LUSC) 8 | #'@name gene_expression 9 | #'@docType data 10 | #'@usage data("gene_expression") 11 | #'@format A data frame with 1305 rows and 5 columns. \describe{ 12 | #' \item{\code{bcr_patient_barcode}}{sample ID} \item{\code{dataset}}{cance type} \item{\code{GATA3}}{GATA3 gene expression} 13 | #' \item{\code{PTEN}}{PTEN gene expression}\item{\code{XBP1}}{XBP1 gene expression.}} 14 | #' 15 | #' @examples 16 | #' data(gene_expression) 17 | #' 18 | #' ggboxplot(gene_expression, x = "dataset", 19 | #' y = c("GATA3", "PTEN", "XBP1"), 20 | #' combine = TRUE, 21 | #' ylab = "Expression", 22 | #' color = "dataset", palette = "jco") 23 | #' 24 | NULL 25 | -------------------------------------------------------------------------------- /R/get_legend.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R 2 | NULL 3 | #' Extract Legends from a ggplot object 4 | #' @description Extract the legend labels from a ggplot object. 5 | #' @param p an object of class ggplot or a list of ggplots. If p is a list, only the first legend is returned. 6 | #' @param position character specifying legend position. Allowed values are one of 7 | #' c("top", "bottom", "left", "right", "none"). To remove the legend use 8 | #' legend = "none". 9 | #' @return an object of class gtable. 10 | #' @examples 11 | #' # Create a scatter plot 12 | #' p <- ggscatter(iris, x = "Sepal.Length", y = "Sepal.Width", 13 | #' color = "Species", palette = "jco", 14 | #' ggtheme = theme_minimal()) 15 | #' p 16 | #' 17 | #' # Extract the legend. Returns a gtable 18 | #' leg <- get_legend(p) 19 | #' 20 | #' # Convert to a ggplot and print 21 | #' as_ggplot(leg) 22 | #' 23 | #' @export 24 | get_legend <- function(p, position = NULL){ 25 | 26 | if(.is_list(p)){ 27 | continue <- TRUE 28 | i <- 1 29 | while(i <= length(p) & continue){ 30 | leg <- .get_legend(p[[i]], position = position) 31 | if(!is.null(leg)) continue <- FALSE 32 | i <- i+1 33 | } 34 | } 35 | else{ 36 | leg <- .get_legend(p, position = position) 37 | } 38 | leg 39 | } 40 | 41 | 42 | 43 | # Return legend for one plot 44 | .get_legend <- function(p, position = NULL){ 45 | 46 | if(is.null(p)) return(NULL) 47 | if(!is.null(position)){ 48 | p <- p + theme(legend.position = position) 49 | } 50 | tmp <- ggplot_gtable(ggplot_build(p)) 51 | leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box") 52 | if(length(leg) > 0) leg <- tmp$grobs[[leg]] 53 | else leg <- NULL 54 | leg 55 | } 56 | 57 | -------------------------------------------------------------------------------- /R/ggpubr-package.R: -------------------------------------------------------------------------------- 1 | #' @keywords internal 2 | #' 3 | #' @details 4 | #' 5 | #' General resources: 6 | #' 7 | #'\itemize{ 8 | #' \item \href{https://rpkgs.datanovia.com/ggpubr/}{ggpubr documentation} 9 | #' \item \href{https://www.datanovia.com/en/blog/tag/ggpubr/}{ggpubr tutorials} 10 | #'} 11 | #' 12 | #' @section Package options: 13 | #' 14 | #' \describe{ 15 | #' \item{ggpubr.parse_aes}{logical indicating whether to parse or not aesthetics variables names. 16 | #' Default is \code{TRUE}. For example, if you want \code{ggpubr} to handle non-standard column names, like \code{A-A}, 17 | #' without parsing, then set this option to \code{FALSE} using \code{options(ggpubr.parse_aes = FALSE)}.} 18 | #' \item{ggpubr.null_device}{A function that creates an appropriate null device. 19 | #' These include: \code{\link[cowplot:pdf_null_device]{cowplot::pdf_null_device}}, 20 | #' \code{\link[cowplot:png_null_device]{cowplot::png_null_device}}, 21 | #' \code{\link[cowplot:cairo_null_device]{cowplot::cairo_null_device}} and 22 | #' \code{\link[cowplot:agg_null_device]{cowplot::agg_null_device}}. Default is 23 | #' \code{\link[cowplot:pdf_null_device]{cowplot::pdf_null_device}}. This is used in 24 | #' function like \code{\link{as_ggplot}()}, which needs to open a graphics 25 | #' device to render ggplot objects into grid graphics objects. This function is 26 | #' used to open null device for avoiding the display of unnecessary blank page 27 | #' when calling \code{\link{ggarrange}()} or \code{\link{as_ggplot}()}} } 28 | #' 29 | "_PACKAGE" 30 | -------------------------------------------------------------------------------- /R/ggpubr_options.R: -------------------------------------------------------------------------------- 1 | #' Global Options for GGPubr 2 | #' @description Displays allowed global options in ggpubr. 3 | #' @examples 4 | #' 5 | #' ggpubr_options() 6 | #' 7 | #' @export 8 | ggpubr_options <- function(){ 9 | list( 10 | ggpubr.parse_aes = TRUE, 11 | ggpubr.null_device = cowplot::pdf_null_device 12 | ) 13 | } 14 | -------------------------------------------------------------------------------- /R/gradient_color.R: -------------------------------------------------------------------------------- 1 | #' @include utilities_color.R 2 | NULL 3 | #'Set Gradient Color 4 | #' 5 | #' @description Change gradient color. 6 | #' \itemize{ 7 | #' \item \code{gradient_color()}: Change gradient color. 8 | #' \item \code{gradient_fill()}: Change gradient fill. 9 | #' } 10 | #' @param palette the color palette to be used for coloring or filling by 11 | #' groups. Allowed values include "grey" for grey color palettes; brewer 12 | #' palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", 13 | #' "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", 14 | #' "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and 15 | #' "rickandmorty". Can be also a numeric vector; in this 16 | #' case a basic color palette is created using the function 17 | #' \link[grDevices]{palette}. 18 | #' 19 | #' @seealso \link{set_palette}. 20 | #' 21 | #' 22 | #'@examples 23 | #' df <- mtcars 24 | #' p <- ggscatter(df, x = "wt", y = "mpg", 25 | #' color = "mpg") 26 | #' 27 | #' # Change gradient color 28 | #' # Use one custom color 29 | #' p + gradient_color("red") 30 | #' 31 | #' # Two colors 32 | #' p + gradient_color(c("blue", "red")) 33 | #' 34 | #' # Three colors 35 | #' p + gradient_color(c("blue", "white", "red")) 36 | #' 37 | #' # Use RColorBrewer palette 38 | #' p + gradient_color("RdYlBu") 39 | #' 40 | #' # Use ggsci color palette 41 | #' p + gradient_color("npg") 42 | #' @rdname gradient_color 43 | #' @export 44 | gradient_color <- function(palette){ 45 | 46 | if(.is_col_palette(palette)) palette <- .get_pal(palette, k = 3) 47 | n_palette <- length(palette) 48 | 49 | if(n_palette == 1) { 50 | palette <- grDevices::colorRampPalette(c("white", palette))(10) 51 | palette <- palette[c(1, 10)] 52 | n_palette <- 2 53 | } 54 | ggplot2::scale_color_gradientn(colours = palette) 55 | } 56 | 57 | #' @rdname gradient_color 58 | #' @export 59 | gradient_fill <- function(palette){ 60 | 61 | if(.is_col_palette(palette)) palette <- .get_pal(palette, k = 3) 62 | n_palette <- length(palette) 63 | 64 | if(n_palette == 1) { 65 | palette <- grDevices::colorRampPalette(c("white", palette))(10) 66 | palette <- palette[c(1, 10)] 67 | n_palette <- 2 68 | } 69 | ggplot2::scale_fill_gradientn(colours = palette) 70 | } 71 | -------------------------------------------------------------------------------- /R/grids.R: -------------------------------------------------------------------------------- 1 | #'Add Grids to a ggplot 2 | #' 3 | #'@description Add grids to ggplot. 4 | #'@param axis axis for which grid should be added. Allowed values include \code{c("xy", "x", "y")}. 5 | #'@param color grid line color. 6 | #'@param size numeric value specifying grid line size. 7 | #'@param linetype line type. An integer (0:8), a name (blank, solid, dashed, 8 | #' dotted, dotdash, longdash, twodash). Sess \code{\link{show_line_types}}. 9 | #' 10 | #' 11 | #'@examples 12 | #'# Load data 13 | #'data("ToothGrowth") 14 | #' 15 | #'# Basic plot 16 | #'p <- ggboxplot(ToothGrowth, x = "dose", y = "len") 17 | #'p 18 | #' 19 | #'# Add border 20 | #' p + grids(linetype = "dashed") 21 | #'@export 22 | grids <- function(axis = c("xy", "x", "y"), color = "grey92", size = NULL, linetype = NULL) 23 | { 24 | axis <- match.arg(axis) 25 | grid.major <- element_line(color = color, size = size, 26 | linetype = linetype) 27 | grid.minor <- element_line(color = color, size = 0.25, 28 | linetype = linetype) 29 | 30 | switch(axis, 31 | xy = theme(panel.grid.major = grid.major, panel.grid.minor = grid.minor), 32 | x = theme(panel.grid.major.x = grid.major, panel.grid.minor.x = grid.minor), 33 | y = theme(panel.grid.major.y = grid.major, panel.grid.minor.y = grid.minor) 34 | ) 35 | } 36 | -------------------------------------------------------------------------------- /R/npc_to_data_coord.R: -------------------------------------------------------------------------------- 1 | #' Convert NPC to Data Coordinates 2 | #' @description Convert NPC (Normalized Parent Coordinates) into data coordinates. 3 | #' @param npc a numeric vector. Each value should be in [0-1] 4 | #' @param data.ranges a numeric vector of length 2 containing the data ranges (minimum and the maximum) 5 | #' @return a numeric vector representing data coordinates. 6 | #' @seealso \code{\link{as_npc}}, \code{\link{get_coord}}. 7 | #' @examples 8 | #' npc_to_data_coord(npc = c(0.2, 0.95), data.ranges = c(1, 20)) 9 | #' as_npc(c("top", "right")) %>% 10 | #' npc_to_data_coord(data.ranges = c(1, 20)) 11 | #' 12 | #' @rdname npc_to_data_coord 13 | #' @export 14 | npc_to_data_coord <- function(npc, data.ranges){ 15 | data.ranges[1] + npc * (data.ranges[2] - data.ranges[1]) 16 | } 17 | -------------------------------------------------------------------------------- /R/reexports.R: -------------------------------------------------------------------------------- 1 | #' @importFrom dplyr mutate 2 | #' @export 3 | dplyr::mutate 4 | #' @importFrom dplyr group_by 5 | #' @export 6 | dplyr::group_by 7 | #' @importFrom rstatix get_summary_stats 8 | #' @export 9 | rstatix::get_summary_stats 10 | -------------------------------------------------------------------------------- /R/rotate.R: -------------------------------------------------------------------------------- 1 | #'Rotate a ggplot Horizontally 2 | #' 3 | #'@description Rotate a ggplot to create horizontal plots. Wrapper around 4 | #' \code{\link[ggplot2]{coord_flip}}. 5 | #'@param ... other arguments to pass to \code{\link[ggplot2]{coord_flip}}. 6 | #' 7 | #'@examples 8 | #'# Load data 9 | #'data("ToothGrowth") 10 | #'df <- ToothGrowth 11 | #' 12 | #'# Basic plot 13 | #'p <- ggboxplot(df, x = "dose", y = "len", 14 | #' color = "dose", palette = "jco") 15 | #'p 16 | #'# Create horizontal plots 17 | #'p + rotate() 18 | #'@export 19 | rotate <- function(...){ 20 | coord_flip(...) 21 | } 22 | -------------------------------------------------------------------------------- /R/rotate_axis_text.R: -------------------------------------------------------------------------------- 1 | #'Rotate Axes Text 2 | #' 3 | #'@description Rotate the x-axis text (tick mark labels). 4 | #'\itemize{ 5 | #'\item \code{rotate_x_text}(): Rotate x axis text. 6 | #'\item \code{rotate_y_text}(): Rotate y axis text. 7 | #'} 8 | #' 9 | #'@param angle numeric value specifying the rotation angle. Default is 90 for vertical x-axis text. 10 | #'@param hjust horizontal justification (in [0, 1]). 11 | #'@param vjust vertical justification (in [0, 1]). 12 | #'@param ... other arguments to pass to the function 13 | #' \code{\link[ggplot2:element]{element_text}()}. 14 | #' 15 | #'@examples 16 | #'# Load data 17 | #'data("ToothGrowth") 18 | #'df <- ToothGrowth 19 | #' 20 | #'# Basic plot 21 | #'p <- ggboxplot(df, x = "dose", y = "len") 22 | #'p 23 | #'# Vertical x axis text 24 | #'p + rotate_x_text() 25 | #'# Set rotation angle to 45 26 | #'p + rotate_x_text(45) 27 | #'p + rotate_y_text(45) 28 | #' 29 | #'@name rotate_axis_text 30 | #'@rdname rotate_axis_text 31 | #'@export 32 | rotate_x_text <- function(angle = 90, hjust = NULL, vjust = NULL, ...){ 33 | 34 | if(missing(hjust) & angle > 5) 35 | hjust <- 1 36 | if(missing(vjust) & angle == 90) 37 | vjust <- 0.5 38 | 39 | theme( 40 | axis.text.x = element_text(angle = angle, hjust = hjust, vjust = vjust, ...) 41 | ) 42 | } 43 | 44 | #'@name rotate_axis_text 45 | #'@rdname rotate_axis_text 46 | #'@export 47 | rotate_y_text <- function(angle = 90, hjust = NULL, vjust = NULL, ...){ 48 | 49 | if(missing(hjust) & angle == 90) 50 | hjust <- 0.5 51 | else if(missing(hjust) & angle > 5) 52 | hjust <- 1 53 | 54 | theme( 55 | axis.text.y = element_text(angle = angle, hjust = hjust, vjust = vjust, ...) 56 | ) 57 | } 58 | -------------------------------------------------------------------------------- /R/show_line_types.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R ggpar.R 2 | NULL 3 | #' Line types available in R 4 | #' @description Show line types available in R. 5 | #' @return a ggplot. 6 | #' 7 | #' @seealso \code{\link{ggpar}} and \code{\link{ggline}}. 8 | #' @examples 9 | #' show_line_types()+ 10 | #' theme_minimal() 11 | #' @export 12 | show_line_types <- function() 13 | { 14 | lt <- c("blank", "solid", "dashed", "dotted", 15 | "dotdash", "longdash", "twodash") 16 | 17 | d <- data.frame(lt = factor(lt, levels = lt)) 18 | 19 | ggplot() + 20 | scale_x_continuous(name="", limits=c(0,1), breaks=NULL) + 21 | scale_linetype_identity() + 22 | geom_segment(data=d, mapping=aes(x=0, xend=1, y=lt, 23 | yend=lt, linetype=lt))+ 24 | labs(title = "Line types available in R", y = "")+ 25 | theme(axis.text.y = element_text(face="bold", color="black")) 26 | } 27 | 28 | 29 | -------------------------------------------------------------------------------- /R/show_point_shapes.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R 2 | NULL 3 | #' Point shapes available in R 4 | #' @description Show point shapes available in R. 5 | #' @return a ggplot. 6 | #' 7 | #' @seealso \code{\link{ggpar}} and \code{\link{ggline}}. 8 | #' @examples 9 | #' show_point_shapes()+ 10 | #' theme_minimal() 11 | #' @export 12 | show_point_shapes <- function() 13 | { 14 | d=data.frame(p=c(0:25)) 15 | p <- ggplot() + 16 | scale_y_continuous(name="") + 17 | scale_x_continuous(name="") + 18 | scale_shape_identity() + 19 | geom_point(data=d, mapping=aes(x=p%%6, y=p%/%6, shape=p), size=5, fill="blue") + 20 | geom_text(data=d, mapping=aes(x=p%%6, y=p%/%6+0.25, label=p), size=3)+ 21 | scale_y_reverse() + 22 | theme( 23 | axis.title = element_blank() 24 | ) 25 | ggpar(p, ticks = FALSE, tickslab = FALSE, 26 | main = "Point shapes available in R") 27 | } 28 | 29 | 30 | -------------------------------------------------------------------------------- /R/stat_chull.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R ggpar.R 2 | NULL 3 | #' Plot convex hull of a set of points 4 | #' @description Plot convex hull of a set of points. 5 | #' @inheritParams ggplot2::layer 6 | #' @inheritParams ggplot2::stat_ellipse 7 | #' @seealso \code{\link{ggpar}}, \code{\link{ggscatter}} 8 | #' @examples 9 | #' # Load data 10 | #' data("mtcars") 11 | #' df <- mtcars 12 | #' df$cyl <- as.factor(df$cyl) 13 | #' 14 | #' # scatter plot with convex hull 15 | #' ggscatter(df, x = "wt", y = "mpg", color = "cyl")+ 16 | #' stat_chull(aes(color = cyl)) 17 | #' 18 | #' ggscatter(df, x = "wt", y = "mpg", color = "cyl")+ 19 | #' stat_chull(aes(color = cyl, fill = cyl), alpha = 0.1, geom = "polygon") 20 | #' 21 | #' @export 22 | stat_chull <- function(mapping = NULL, data = NULL, geom = "path", 23 | position = "identity", na.rm = FALSE, show.legend = NA, 24 | inherit.aes = TRUE, ...) { 25 | layer( 26 | stat = StatChull, data = data, mapping = mapping, geom = geom, 27 | position = position, show.legend = show.legend, inherit.aes = inherit.aes, 28 | params = list(na.rm = na.rm, ...) 29 | ) 30 | } 31 | 32 | # Convex ellipse 33 | StatChull <- ggproto("StatChull", Stat, 34 | compute_group = function(data, scales) { 35 | data[chull(data$x, data$y), , drop = FALSE] 36 | }, 37 | required_aes = c("x", "y") 38 | ) 39 | 40 | -------------------------------------------------------------------------------- /R/stat_mean.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R 2 | NULL 3 | #' Draw group mean points 4 | #' @description Draw the mean point of each group. 5 | #' @inheritParams ggplot2::layer 6 | #' @param ... other arguments to pass to \code{\link[ggplot2]{geom_point}}. 7 | #' @param na.rm If FALSE (the default), removes missing values with a warning. 8 | #' If TRUE silently removes missing values. 9 | #' @seealso \code{\link{stat_conf_ellipse}}, \code{\link{stat_chull}} and 10 | #' \code{\link{ggscatter}} 11 | #' @examples 12 | #' # Load data 13 | #' data("mtcars") 14 | #' df <- mtcars 15 | #' df$cyl <- as.factor(df$cyl) 16 | #' 17 | #' # Scatter plot with ellipses and group mean points 18 | #' ggscatter(df, x = "wt", y = "mpg", 19 | #' color = "cyl", shape = "cyl", ellipse = TRUE)+ 20 | #' stat_mean(aes(color = cyl, shape = cyl), size = 4) 21 | #' 22 | #' @export 23 | stat_mean <- function(mapping = NULL, data = NULL, geom = "point", 24 | position = "identity", na.rm = FALSE, show.legend = NA, 25 | inherit.aes = TRUE, ...) { 26 | layer( 27 | stat = StatMean, data = data, mapping = mapping, geom = geom, 28 | position = position, show.legend = show.legend, inherit.aes = inherit.aes, 29 | params = list(na.rm = na.rm, ...) 30 | ) 31 | } 32 | 33 | 34 | StatMean<- ggproto("StatMean", Stat, 35 | required_aes = c("x", "y"), 36 | compute_group = function(data, scales) { 37 | res <- data.frame(x = mean(data$x, na.rm = TRUE), 38 | y = mean(data$y, na.rm = TRUE)) 39 | res 40 | } 41 | ) 42 | -------------------------------------------------------------------------------- /R/stat_overlay_normal_density.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R 2 | NULL 3 | #' Overlay Normal Density Plot 4 | #' 5 | #' @description Overlay normal density plot (with the same mean and SD) to the 6 | #' density distribution of 'x'. This is useful for visually inspecting the 7 | #' degree of deviance from normality. 8 | #' @inheritParams ggplot2::layer 9 | #' @param ... other arguments to pass to \code{\link[ggplot2:geom_path]{geom_line}}. 10 | #' @param na.rm If FALSE (the default), removes missing values with a warning. 11 | #' If TRUE silently removes missing values. 12 | #' @seealso \code{\link{ggdensity}} 13 | #' @examples 14 | #' # Simpledensity plot 15 | #' data("mtcars") 16 | #' ggdensity(mtcars, x = "mpg", fill = "red") + 17 | #' scale_x_continuous(limits = c(-1, 50)) + 18 | #' stat_overlay_normal_density(color = "red", linetype = "dashed") 19 | #' 20 | #' # Color by groups 21 | #' data(iris) 22 | #' ggdensity(iris, "Sepal.Length", color = "Species") + 23 | #' stat_overlay_normal_density(aes(color = Species), linetype = "dashed") 24 | #' 25 | #' 26 | #' # Facet 27 | #' ggdensity(iris, "Sepal.Length", facet.by = "Species") + 28 | #' stat_overlay_normal_density(color = "red", linetype = "dashed") 29 | #' 30 | #' @export 31 | stat_overlay_normal_density <- function(mapping = NULL, data = NULL, geom = "line", 32 | position = "identity", na.rm = FALSE, show.legend = NA, 33 | inherit.aes = TRUE, ...) { 34 | if(is.null(mapping)){ 35 | mapping <- ggplot2::aes(y = NULL) 36 | }else{ 37 | mapping["y"] <- list(NULL) 38 | } 39 | layer( 40 | stat = StatOverlayNormalDensity, data = data, mapping = mapping, geom = geom, 41 | position = position, show.legend = show.legend, inherit.aes = inherit.aes, 42 | params = list(na.rm = na.rm, ...) 43 | ) 44 | } 45 | 46 | 47 | StatOverlayNormalDensity<- ggproto("StatOverlayNormalDensity", Stat, 48 | required_aes = c("x"), 49 | compute_group = function(data, scales) { 50 | x <- data$x 51 | .mean <- mean(x, na.rm = TRUE) 52 | .sd <- stats::sd(x, na.rm = TRUE) 53 | probability.points <- stats::ppoints(length(x[!(is.na(x))])) 54 | res.density <- stats::density(stats::qnorm(probability.points, .mean, .sd)) 55 | res.density <- data.frame(x = res.density$x, y = res.density$y) 56 | res.density 57 | } 58 | ) 59 | -------------------------------------------------------------------------------- /R/stat_stars.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R 2 | NULL 3 | #' Add Stars to a Scatter Plot 4 | #' @description Create a star plot by drawing segments from group centroid to each points. 5 | #' @inheritParams ggplot2::layer 6 | #' @param ... other arguments to pass to \code{\link[ggplot2]{geom_segment}}. 7 | #' @param na.rm If FALSE (the default), removes missing values with a warning. 8 | #' If TRUE silently removes missing values. 9 | #' @seealso \code{\link{ggscatter}} 10 | #' @examples 11 | #' # Load data 12 | #' data("mtcars") 13 | #' df <- mtcars 14 | #' df$cyl <- as.factor(df$cyl) 15 | #' 16 | #' # Scatter plot with ellipses and group mean points 17 | #' ggscatter(df, x = "wt", y = "mpg", 18 | #' color = "cyl", shape = "cyl", 19 | #' mean.point = TRUE, ellipse = TRUE)+ 20 | #' stat_stars(aes(color = cyl)) 21 | #' 22 | #' @export 23 | stat_stars <- function(mapping = NULL, data = NULL, geom = "segment", 24 | position = "identity", na.rm = FALSE, show.legend = NA, 25 | inherit.aes = TRUE, ...) { 26 | layer( 27 | stat = StatStars, data = data, mapping = mapping, geom = geom, 28 | position = position, show.legend = show.legend, inherit.aes = inherit.aes, 29 | params = list(na.rm = na.rm, ...) 30 | ) 31 | } 32 | 33 | 34 | StatStars<- ggproto("StatStars", Stat, 35 | required_aes = c("x", "y"), 36 | compute_group = function(data, scales) { 37 | x.mean <- mean(data$x, na.rm = TRUE) 38 | y.mean <- mean(data$y, na.rm = TRUE) 39 | res <- data %>% mutate(x = x.mean, y = y.mean) 40 | res$xend <- data$x 41 | res$yend <- data$y 42 | res 43 | } 44 | ) 45 | -------------------------------------------------------------------------------- /R/text_grob.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R 2 | NULL 3 | 4 | #' Create a Text Graphical object 5 | #' @description Create easily a customized text grob (graphical object). Wrapper around 6 | #' \code{\link[grid:grid.text]{textGrob}}. 7 | #' @inheritParams grid::grid.text 8 | #' @param color text font color. 9 | #' @param face font face. Allowed values include one of \code{"plain", "bold", 10 | #' "italic", "bold.italic"}. 11 | #' @param size font size (e.g.: size = 12) 12 | #' @param lineheight line height (e.g.: lineheight = 2). 13 | #' @param family font family. 14 | #' @param ... other arguments passed to \link[grid:grid.text]{textGrob}. 15 | #' @return a text grob. 16 | #' @examples 17 | #'text <- paste("iris data set gives the measurements in cm", 18 | #' "of the variables sepal length and width", 19 | #' "and petal length and width, respectively,", 20 | #' "for 50 flowers from each of 3 species of iris.", 21 | #' "The species are Iris setosa, versicolor, and virginica.", sep = "\n") 22 | #' 23 | #'# Create a text grob 24 | #'tgrob <- text_grob(text, face = "italic", color = "steelblue") 25 | #'# Draw the text 26 | #'as_ggplot(tgrob) 27 | #' 28 | #' @export 29 | text_grob <- function(label, just = "centre", hjust = NULL, vjust = NULL, rot = 0, 30 | color = "black", face = "plain", size = NULL, lineheight = NULL, 31 | family = NULL, ...) 32 | { 33 | 34 | gp <- grid::gpar(col = color, fontface = face, fontsize = size, 35 | lineheight = lineheight, fontfamily = family) 36 | 37 | tgrob <- grid::textGrob(label = label, just = just, hjust = hjust, vjust = vjust, 38 | rot = rot, gp = gp, ...) 39 | tgrob 40 | } 41 | -------------------------------------------------------------------------------- /R/theme_transparent.R: -------------------------------------------------------------------------------- 1 | #' @include utilities.R 2 | #' @import ggplot2 3 | NULL 4 | #'Create a ggplot with Transparent Background 5 | #' 6 | #'@description Create a ggplot with transparent background. 7 | #'@param base_size base font size 8 | #'@param base_family base font family 9 | #'@seealso \code{\link{theme_pubr}} 10 | #' @examples 11 | #'# Create a scatter plot 12 | #'sp <- ggscatter(iris, x = "Sepal.Length", y = "Sepal.Width", 13 | #' color = "Species", palette = "jco", 14 | #' size = 3, alpha = 0.6) 15 | #'sp 16 | #' 17 | #'# Transparent theme 18 | #'sp + theme_transparent() 19 | #' 20 | #'@export 21 | theme_transparent <- function (base_size = 12, base_family = "") 22 | { 23 | theme_classic(base_size = base_size, base_family = base_family) + 24 | theme( 25 | panel.background = element_rect(fill = "transparent", colour = NA), 26 | plot.background = element_rect(fill = "transparent", colour = NA), 27 | legend.background = element_rect(fill = "transparent", colour = NA), 28 | legend.box.background = element_rect(fill = "transparent", colour = NA), 29 | axis.line = element_blank(), 30 | axis.title = element_blank(), 31 | plot.title = element_blank(), 32 | axis.text = element_blank(), 33 | axis.ticks = element_blank() 34 | ) 35 | } 36 | -------------------------------------------------------------------------------- /R/utils-aes.R: -------------------------------------------------------------------------------- 1 | # Extract group name from mapping, aes 2 | aes_get_group <- function(mapping){ 3 | group <- NULL 4 | if(!is.null(mapping)){ 5 | if(!is.null(mapping$group)) group <- rlang::as_label(mapping$group) 6 | } 7 | group 8 | } 9 | -------------------------------------------------------------------------------- /R/utils-geom-signif.R: -------------------------------------------------------------------------------- 1 | #' geom_signif exported from ggsignif package 2 | #' 3 | #' See \code{ggsignif::\link[ggsignif:stat_signif]{geom_signif}} for details. 4 | #' 5 | #' @name geom_signif 6 | #' @rdname geom_signif 7 | #' @keywords internal 8 | #' @export 9 | #' @importFrom ggsignif geom_signif 10 | NULL 11 | -------------------------------------------------------------------------------- /R/utils-pipe.R: -------------------------------------------------------------------------------- 1 | #' Pipe operator 2 | #' 3 | #' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details. 4 | #' 5 | #' @name %>% 6 | #' @rdname pipe 7 | #' @keywords internal 8 | #' @export 9 | #' @importFrom magrittr %>% 10 | #' @usage lhs \%>\% rhs 11 | NULL 12 | -------------------------------------------------------------------------------- /R/utils-tidyr.R: -------------------------------------------------------------------------------- 1 | # Transform data into long format-------------------- 2 | # Replacement of deprecated tidyr::gather_() 3 | # wrapper around tidyr::pivot_longer() but using `cols_vary = "slowest"` as default 4 | # instead of `cols_vary = "fastest"` 5 | df_gather <- function(data, cols, cols_vary = "slowest", 6 | names_to = "name", values_to = "value", ...){ 7 | data %>% 8 | tidyr::pivot_longer( 9 | cols = dplyr::all_of(cols), names_to = names_to, values_to = values_to, 10 | cols_vary = cols_vary, ... 11 | ) 12 | } 13 | -------------------------------------------------------------------------------- /cran-comments.md: -------------------------------------------------------------------------------- 1 | ## Test environments 2 | * local OS X install, R 3.6.0 3 | * win-builder 4 | * Travis 5 | 6 | ## R CMD check results 7 | There were no ERRORs, WARNINGs or NOTEs. 8 | 9 | ## Downstream dependencies 10 | I have also run R CMD check on downstream dependencies of ggpubr. 11 | All packages that I could install passed. 12 | 13 | ## Update 14 | 15 | This is an updated version 0.6.0 (see NEWS.md). 16 | 17 | ## Resubmission 18 | 19 | 20 | This is a resubmission of version 0.6.0 . In this version I have: 21 | 22 | * fixed issues so that the downstream dependencies `tinyarray` passed R CMD check 23 | * Note that the issue concerning the "VALERIE" package is not related to ggpubr. This issue is a false positive 24 | -------------------------------------------------------------------------------- /data-raw/gene_expression.R: -------------------------------------------------------------------------------- 1 | library(RTCGA) 2 | library(RTCGA.mRNA) 3 | gene_expression <- expressionsTCGA(BRCA.mRNA, OV.mRNA, LUSC.mRNA, 4 | extract.cols = c("GATA3", "PTEN", "XBP1")) 5 | 6 | # Number of samples 7 | nb_samples <- table(expr$dataset) 8 | nb_samples 9 | 10 | # simplify data set names by removing the “mRNA” tag. 11 | gene_expression$dataset <- gsub(pattern = ".mRNA", replacement = "", expr$dataset) 12 | # simplify also the patients’ barcode column. 13 | gene_expression$bcr_patient_barcode <- paste0(gene_expression$dataset, c(1:590, 1:561, 1:154)) 14 | 15 | usethis::use_data(gene_expression, overwrite = TRUE) 16 | -------------------------------------------------------------------------------- /data/diff_express.rda: 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58 | nav[data-toggle='toc'] .nav > .active > ul { 59 | display: block; 60 | } 61 | -------------------------------------------------------------------------------- /docs/docsearch.js: -------------------------------------------------------------------------------- 1 | $(function() { 2 | 3 | // register a handler to move the focus to the search bar 4 | // upon pressing shift + "/" (i.e. "?") 5 | $(document).on('keydown', function(e) { 6 | if (e.shiftKey && e.keyCode == 191) { 7 | e.preventDefault(); 8 | $("#search-input").focus(); 9 | } 10 | }); 11 | 12 | $(document).ready(function() { 13 | // do keyword highlighting 14 | /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */ 15 | var mark = function() { 16 | 17 | var referrer = document.URL ; 18 | var paramKey = "q" ; 19 | 20 | if (referrer.indexOf("?") !== -1) { 21 | var qs = referrer.substr(referrer.indexOf('?') + 1); 22 | var qs_noanchor = qs.split('#')[0]; 23 | var qsa = qs_noanchor.split('&'); 24 | var keyword = ""; 25 | 26 | for (var i = 0; i < qsa.length; i++) { 27 | var currentParam = qsa[i].split('='); 28 | 29 | if (currentParam.length !== 2) { 30 | continue; 31 | } 32 | 33 | if (currentParam[0] == paramKey) { 34 | keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20")); 35 | } 36 | } 37 | 38 | if (keyword !== "") { 39 | $(".contents").unmark({ 40 | done: function() { 41 | $(".contents").mark(keyword); 42 | } 43 | }); 44 | } 45 | } 46 | }; 47 | 48 | mark(); 49 | }); 50 | }); 51 | 52 | /* Search term highlighting ------------------------------*/ 53 | 54 | function matchedWords(hit) { 55 | var words = []; 56 | 57 | var hierarchy = hit._highlightResult.hierarchy; 58 | // loop to fetch from lvl0, lvl1, etc. 59 | for (var idx in hierarchy) { 60 | words = words.concat(hierarchy[idx].matchedWords); 61 | } 62 | 63 | var content = hit._highlightResult.content; 64 | if (content) { 65 | words = words.concat(content.matchedWords); 66 | } 67 | 68 | // return unique words 69 | var words_uniq = [...new Set(words)]; 70 | return words_uniq; 71 | } 72 | 73 | function updateHitURL(hit) { 74 | 75 | var words = matchedWords(hit); 76 | var url = ""; 77 | 78 | if (hit.anchor) { 79 | url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor; 80 | } else { 81 | url = hit.url + '?q=' + escape(words.join(" ")); 82 | } 83 | 84 | return url; 85 | } 86 | -------------------------------------------------------------------------------- /docs/docsearch.json: -------------------------------------------------------------------------------- 1 | { 2 | "index_name": "ggpubr", 3 | "start_urls": [ 4 | { 5 | "url": "/index.html", 6 | "selectors_key": "homepage", 7 | "tags": [ 8 | "homepage" 9 | ] 10 | }, 11 | { 12 | "url": "/reference", 13 | "selectors_key": "reference", 14 | "tags": [ 15 | "reference" 16 | ] 17 | }, 18 | { 19 | "url": "/articles", 20 | "selectors_key": "articles", 21 | "tags": [ 22 | "articles" 23 | ] 24 | } 25 | ], 26 | "stop_urls": [ 27 | "/reference/$", 28 | "/reference/index.html", 29 | "/articles/$", 30 | "/articles/index.html" 31 | ], 32 | "sitemap_urls": [ 33 | "/sitemap.xml" 34 | ], 35 | "selectors": { 36 | "homepage": { 37 | "lvl0": { 38 | "selector": ".contents h1", 39 | "default_value": "ggpubr Home page" 40 | }, 41 | "lvl1": { 42 | "selector": ".contents h2" 43 | }, 44 | "lvl2": { 45 | "selector": ".contents h3", 46 | "default_value": "Context" 47 | }, 48 | "lvl3": ".ref-arguments td, .ref-description", 49 | "text": ".contents p, .contents li, .contents .pre" 50 | }, 51 | "reference": { 52 | "lvl0": { 53 | "selector": ".contents h1" 54 | }, 55 | "lvl1": { 56 | "selector": ".contents .name", 57 | "default_value": "Argument" 58 | }, 59 | "lvl2": { 60 | "selector": ".ref-arguments th", 61 | "default_value": "Description" 62 | }, 63 | "lvl3": ".ref-arguments td, .ref-description", 64 | "text": ".contents p, .contents li" 65 | }, 66 | "articles": { 67 | "lvl0": { 68 | "selector": ".contents h1" 69 | }, 70 | "lvl1": { 71 | "selector": 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-------------------------------------------------------------------------------- /ggpubr.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | 18 | BuildType: Package 19 | PackageUseDevtools: Yes 20 | PackageInstallArgs: --no-multiarch --with-keep.source 21 | -------------------------------------------------------------------------------- /images/adjusted-p-value-box-plot-faceted.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kassambara/ggpubr/6aeb4f701399929b130917e797658819c71a2304/images/adjusted-p-value-box-plot-faceted.jpeg 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-------------------------------------------------------------------------------- /inst/images/background-image.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kassambara/ggpubr/6aeb4f701399929b130917e797658819c71a2304/inst/images/background-image.png -------------------------------------------------------------------------------- /man/as_ggplot.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/as_ggplot.R 3 | \name{as_ggplot} 4 | \alias{as_ggplot} 5 | \title{Storing grid.arrange() arrangeGrob() and plots} 6 | \usage{ 7 | as_ggplot(x) 8 | } 9 | \arguments{ 10 | \item{x}{an object of class gtable or grob as returned by the functions 11 | \code{\link[gridExtra:arrangeGrob]{arrangeGrob}()} and 12 | \code{\link[gridExtra:arrangeGrob]{grid.arrange}()}.} 13 | } 14 | \value{ 15 | an object of class ggplot. 16 | } 17 | \description{ 18 | Transform the output of 19 | \code{\link[gridExtra:arrangeGrob]{arrangeGrob}()} and 20 | \code{\link[gridExtra:arrangeGrob]{grid.arrange}()} to a an object of class 21 | ggplot. 22 | } 23 | \examples{ 24 | # Creat some plots 25 | bxp <- ggboxplot(iris, x = "Species", y = "Sepal.Length") 26 | vp <- ggviolin(iris, x = "Species", y = "Sepal.Length", 27 | add = "mean_sd") 28 | 29 | # Arrange the plots in one page 30 | # Returns a gtable (grob) object 31 | library(gridExtra) 32 | gt <- arrangeGrob(bxp, vp, ncol = 2) 33 | 34 | # Transform to a ggplot and print 35 | as_ggplot(gt) 36 | 37 | } 38 | -------------------------------------------------------------------------------- /man/as_npc.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/as_npc.R 3 | \name{as_npc} 4 | \alias{as_npc} 5 | \alias{as_npcx} 6 | \alias{as_npcy} 7 | \title{Convert Character Coordinates into Normalized Parent Coordinates (NPC)} 8 | \usage{ 9 | as_npc( 10 | value, 11 | group = 1L, 12 | step = 0.1, 13 | margin.npc = 0.05, 14 | axis = c("xy", "x", "y") 15 | ) 16 | 17 | as_npcx(value, group = 1L, step = 0.1, margin.npc = 0.05) 18 | 19 | as_npcy(value, group = 1L, step = 0.1, margin.npc = 0.05) 20 | } 21 | \arguments{ 22 | \item{value}{numeric (in [0-1]) or character vector of coordinates. If 23 | character, should be one of \code{c('right', 'left', 'bottom', 'top', 24 | 'center', 'centre', 'middle')}.} 25 | 26 | \item{group}{integer ggplot's group id. Used to shift coordinates to avoid 27 | overlaps.} 28 | 29 | \item{step}{numeric value in [0-1]. The step size for shifting coordinates 30 | in npc units. Considered as horizontal step for x-axis and vertical step 31 | for y-axis. For y-axis, the step value can be negative to reverse the order of groups.} 32 | 33 | \item{margin.npc}{numeric [0-1] The margin added towards the nearest 34 | plotting area edge when converting character coordinates into npc.} 35 | 36 | \item{axis}{the concerned axis . Should be one of \code{c("xy", "x", "y")}.} 37 | } 38 | \value{ 39 | A numeric vector with values in the range [0-1] representing npc 40 | coordinates. 41 | } 42 | \description{ 43 | Convert character coordinates to npc units and shift postions to avoid 44 | overlaps when grouping is active. If numeric validate npc values. 45 | } 46 | \details{ 47 | the \code{as_npc()} function is an adaptation from 48 | \code{ggpmisc::compute_npc()}. 49 | } 50 | \section{Functions}{ 51 | \itemize{ 52 | \item \code{as_npc()}: converts x or y coordinate values into npc. Input values 53 | should be numeric or one of the following values \code{c('right', 'left', 54 | 'bottom', 'top', 'center', 'centre', 'middle')}. 55 | 56 | \item \code{as_npcx()}: converts x coordinate values into npc. Input values should 57 | be numeric or one of the following values \code{c('right', 'left', 58 | 'center', 'centre', 'middle')}. Wrapper around \code{as_npc(axis = "x")}. 59 | 60 | \item \code{as_npcy()}: converts y coordinate values into npc. Input values should 61 | be numeric or one of the following values \code{c( 'bottom', 'top', 62 | 'center', 'centre', 'middle')}. Wrapper around \code{as_npc(axis = "y")}. 63 | 64 | }} 65 | \examples{ 66 | as_npc(c("left", "right")) 67 | as_npc(c("top", "right")) 68 | 69 | } 70 | \seealso{ 71 | \code{\link{npc_to_data_coord}}, \code{\link{get_coord}}. 72 | } 73 | -------------------------------------------------------------------------------- /man/axis_scale.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/axis_scale.R 3 | \name{axis_scale} 4 | \alias{axis_scale} 5 | \alias{xscale} 6 | \alias{yscale} 7 | \title{Change Axis Scale: log2, log10 and more} 8 | \usage{ 9 | xscale(.scale, .format = FALSE) 10 | 11 | yscale(.scale, .format = FALSE) 12 | } 13 | \arguments{ 14 | \item{.scale}{axis scale. Allowed values are one of c("none", "log2", "log10", 15 | "sqrt", "percent", "dollar", "scientific"); e.g.: .scale="log2".} 16 | 17 | \item{.format}{ogical value. If TRUE, axis tick mark labels will be formatted 18 | when .scale = "log2" or "log10".} 19 | } 20 | \description{ 21 | Change axis scale. 22 | \itemize{ 23 | \item \code{xscale}: change x axis scale. 24 | \item \code{yscale}: change y axis scale. 25 | } 26 | } 27 | \examples{ 28 | # Basic scatter plots 29 | data(cars) 30 | p <- ggscatter(cars, x = "speed", y = "dist") 31 | p 32 | 33 | # Set log scale 34 | p + yscale("log2", .format = TRUE) 35 | } 36 | -------------------------------------------------------------------------------- /man/background_image.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/background_image.R 3 | \name{background_image} 4 | \alias{background_image} 5 | \title{Add Background Image to ggplot2} 6 | \usage{ 7 | background_image(raster.img) 8 | } 9 | \arguments{ 10 | \item{raster.img}{raster object to display, as returned by the function 11 | \code{readPNG()}[in \code{png} package] and \code{readJPEG()} [in \code{jpeg} package].} 12 | } 13 | \description{ 14 | Add background image to ggplot2. 15 | } 16 | \examples{ 17 | \dontrun{ 18 | install.packages("png") 19 | 20 | # Import the image 21 | img.file <- system.file(file.path("images", "background-image.png"), 22 | package = "ggpubr") 23 | img <- png::readPNG(img.file) 24 | 25 | # Plot with background image 26 | ggplot(iris, aes(Species, Sepal.Length))+ 27 | background_image(img)+ 28 | geom_boxplot(aes(fill = Species), color = "white")+ 29 | fill_palette("jco") 30 | } 31 | 32 | } 33 | \author{ 34 | Alboukadel Kassambara 35 | } 36 | -------------------------------------------------------------------------------- /man/bgcolor.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/bgcolor.R 3 | \name{bgcolor} 4 | \alias{bgcolor} 5 | \title{Change ggplot Panel Background Color} 6 | \usage{ 7 | bgcolor(color) 8 | } 9 | \arguments{ 10 | \item{color}{background color.} 11 | } 12 | \description{ 13 | Change ggplot panel background color. 14 | } 15 | \examples{ 16 | # Load data 17 | data("ToothGrowth") 18 | df <- ToothGrowth 19 | 20 | # Basic plot 21 | p <- ggboxplot(df, x = "dose", y = "len") 22 | p 23 | 24 | # Change panel background color 25 | p + 26 | bgcolor("#BFD5E3")+ 27 | border("#BFD5E3") 28 | } 29 | \seealso{ 30 | \link{border}(). 31 | } 32 | -------------------------------------------------------------------------------- /man/border.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/border.R 3 | \name{border} 4 | \alias{border} 5 | \title{Set ggplot Panel Border Line} 6 | \usage{ 7 | border(color = "black", size = 0.8, linetype = NULL) 8 | } 9 | \arguments{ 10 | \item{color}{border line color.} 11 | 12 | \item{size}{numeric value specifying border line size.} 13 | 14 | \item{linetype}{line type. An integer (0:8), a name (blank, solid, dashed, 15 | dotted, dotdash, longdash, twodash). Sess \code{\link{show_line_types}}.} 16 | } 17 | \description{ 18 | Change or set ggplot panel border. 19 | } 20 | \examples{ 21 | # Load data 22 | data("ToothGrowth") 23 | df <- ToothGrowth 24 | 25 | # Basic plot 26 | p <- ggboxplot(df, x = "dose", y = "len") 27 | p 28 | 29 | # Add border 30 | p + border() 31 | } 32 | -------------------------------------------------------------------------------- /man/create_aes.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/create_aes.R 3 | \name{create_aes} 4 | \alias{create_aes} 5 | \title{Create Aes Mapping from a List} 6 | \usage{ 7 | create_aes(.list, parse = TRUE) 8 | } 9 | \arguments{ 10 | \item{.list}{a list of aesthetic arguments; for example .list = list(x = "dose", y = "len", color = "dose").} 11 | 12 | \item{parse}{logical. If TRUE, parse the input as an expression.} 13 | } 14 | \description{ 15 | Create aes mapping to make programming easy with ggplot2. 16 | } 17 | \examples{ 18 | # Simple aes creation 19 | create_aes(list(x = "Sepal.Length", y = "Petal.Length" )) 20 | 21 | # Parse an expression 22 | x <- "log2(Sepal.Length)" 23 | y <- "log2(Petal.Length)" 24 | create_aes(list(x = x, y = y ), parse = TRUE) 25 | 26 | # Create a ggplot 27 | mapping <- create_aes(list(x = x, y = y ), parse = TRUE) 28 | ggplot(iris, mapping) + 29 | geom_point() 30 | 31 | } 32 | -------------------------------------------------------------------------------- /man/desc_statby.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/desc_statby.R 3 | \name{desc_statby} 4 | \alias{desc_statby} 5 | \title{Descriptive statistics by groups} 6 | \usage{ 7 | desc_statby(data, measure.var, grps, ci = 0.95) 8 | } 9 | \arguments{ 10 | \item{data}{a data frame.} 11 | 12 | \item{measure.var}{the name of a column containing the variable to be summarized.} 13 | 14 | \item{grps}{a character vector containing grouping variables; e.g.: grps = c("grp1", "grp2")} 15 | 16 | \item{ci}{the percent range of the confidence interval (default is 0.95).} 17 | } 18 | \value{ 19 | A data frame containing descriptive statistics, such as: 20 | \itemize{ 21 | \item \strong{length}: the number of elements in each group 22 | \item \strong{min}: minimum 23 | \item \strong{max}: maximum 24 | \item \strong{median}: median 25 | \item \strong{mean}: mean 26 | \item \strong{iqr}: interquartile range 27 | \item \strong{mad}: median absolute deviation (see ?MAD) 28 | \item \strong{sd}: standard deviation of the sample 29 | \item \strong{se}: standard error of the mean. It's calculated as the sample standard deviation divided by the root of the sample size. 30 | \item \strong{ci}: confidence interval of the mean 31 | \item \strong{range}: the range = max - min 32 | \item \strong{cv}: coefficient of variation, sd/mean 33 | \item \strong{var}: variance, sd^2 34 | } 35 | } 36 | \description{ 37 | Computes descriptive statistics by groups for a measure variable. 38 | } 39 | \examples{ 40 | # Load data 41 | data("ToothGrowth") 42 | 43 | # Descriptive statistics 44 | res <- desc_statby(ToothGrowth, measure.var = "len", 45 | grps = c("dose", "supp")) 46 | head(res[, 1:10]) 47 | 48 | } 49 | -------------------------------------------------------------------------------- /man/diff_express.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/diff_express.R 3 | \docType{data} 4 | \name{diff_express} 5 | \alias{diff_express} 6 | \title{Differential gene expression analysis results} 7 | \format{ 8 | A data frame with 36028 rows and 5 columns. \describe{ 9 | \item{\code{name}}{gene names} \item{\code{baseMean}}{mean expression 10 | signal across all samples} \item{\code{log2FoldChange}}{log2 fold change} 11 | \item{\code{padj}}{Adjusted p-value}\item{\code{detection_call}}{a numeric 12 | vector specifying whether the genes is expressed (value = 1) or not (value = 0).}} 13 | } 14 | \usage{ 15 | data("diff_express") 16 | } 17 | \description{ 18 | Differential gene expression analysis results obtained from 19 | comparing the RNAseq data of two different cell populations using DESeq2 20 | } 21 | \examples{ 22 | data(diff_express) 23 | 24 | # Default plot 25 | ggmaplot(diff_express, main = expression("Group 1" \%->\% "Group 2"), 26 | fdr = 0.05, fc = 2, size = 0.4, 27 | palette = c("#B31B21", "#1465AC", "darkgray"), 28 | genenames = as.vector(diff_express$name), 29 | legend = "top", top = 20, 30 | font.label = c("bold", 11), 31 | font.legend = "bold", 32 | font.main = "bold", 33 | ggtheme = ggplot2::theme_minimal()) 34 | 35 | # Add rectangle around labesl 36 | ggmaplot(diff_express, main = expression("Group 1" \%->\% "Group 2"), 37 | fdr = 0.05, fc = 2, size = 0.4, 38 | palette = c("#B31B21", "#1465AC", "darkgray"), 39 | genenames = as.vector(diff_express$name), 40 | legend = "top", top = 20, 41 | font.label = c("bold", 11), label.rectangle = TRUE, 42 | font.legend = "bold", 43 | font.main = "bold", 44 | ggtheme = ggplot2::theme_minimal()) 45 | 46 | } 47 | -------------------------------------------------------------------------------- /man/gene_citation.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/gene_citation.R 3 | \docType{data} 4 | \name{gene_citation} 5 | \alias{gene_citation} 6 | \title{Gene Citation Index} 7 | \format{ 8 | A data frame with 66 rows and 2 columns. \describe{ 9 | \item{\code{gene}}{gene names} \item{\code{citation_index}}{mean citation index} } 10 | } 11 | \usage{ 12 | data("gene_citation") 13 | } 14 | \description{ 15 | Contains the mean citation index of 66 genes obtained by 16 | assessing PubMed abstracts and annotations using two key words i) Gene name 17 | + b cell differentiation and ii) Gene name + plasma cell differentiation. 18 | } 19 | \examples{ 20 | data(gene_citation) 21 | 22 | # Some key genes of interest to be highlighted 23 | key.gns <- c("MYC", "PRDM1", "CD69", "IRF4", "CASP3", "BCL2L1", "MYB", "BACH2", "BIM1", "PTEN", 24 | "KRAS", "FOXP1", "IGF1R", "KLF4", "CDK6", "CCND2", "IGF1", "TNFAIP3", "SMAD3", "SMAD7", 25 | "BMPR2", "RB1", "IGF2R", "ARNT") 26 | # Density distribution 27 | ggdensity(gene_citation, x = "citation_index", y = "..count..", 28 | xlab = "Number of citation", 29 | ylab = "Number of genes", 30 | fill = "lightgray", color = "black", 31 | label = "gene", label.select = key.gns, repel = TRUE, 32 | font.label = list(color= "citation_index"), 33 | xticks.by = 20, # Break x ticks by 20 34 | gradient.cols = c("blue", "red"), 35 | legend = "bottom", 36 | legend.title = "" # Hide legend title 37 | ) 38 | 39 | } 40 | -------------------------------------------------------------------------------- /man/gene_expression.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/gene_expression.R 3 | \docType{data} 4 | \name{gene_expression} 5 | \alias{gene_expression} 6 | \title{Gene Expression Data} 7 | \format{ 8 | A data frame with 1305 rows and 5 columns. \describe{ 9 | \item{\code{bcr_patient_barcode}}{sample ID} \item{\code{dataset}}{cance type} \item{\code{GATA3}}{GATA3 gene expression} 10 | \item{\code{PTEN}}{PTEN gene expression}\item{\code{XBP1}}{XBP1 gene expression.}} 11 | } 12 | \usage{ 13 | data("gene_expression") 14 | } 15 | \description{ 16 | Gene expression data extracted from TCGA using the `RTCGA` and 17 | `RTCGA.mRNA` R packages. It contains the mRNA expression for 3 genes - 18 | GATA3, PTEN and XBP1- from 3 different datasets: Breast invasive carcinoma 19 | (BRCA), Ovarian serous cystadenocarcinoma (OV) and Lung squamous cell 20 | carcinoma (LUSC) 21 | } 22 | \examples{ 23 | data(gene_expression) 24 | 25 | ggboxplot(gene_expression, x = "dataset", 26 | y = c("GATA3", "PTEN", "XBP1"), 27 | combine = TRUE, 28 | ylab = "Expression", 29 | color = "dataset", palette = "jco") 30 | 31 | } 32 | -------------------------------------------------------------------------------- /man/geom_exec.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/geom_exec.R 3 | \name{geom_exec} 4 | \alias{geom_exec} 5 | \title{Execute ggplot2 functions} 6 | \usage{ 7 | geom_exec(geomfunc = NULL, data = NULL, position = NULL, ...) 8 | } 9 | \arguments{ 10 | \item{geomfunc}{a ggplot2 function (e.g.: geom_point)} 11 | 12 | \item{data}{a data frame to be used for mapping} 13 | 14 | \item{position}{Position adjustment, either as a string, or the result of a 15 | call to a position adjustment function.} 16 | 17 | \item{...}{arguments accepted by the function} 18 | } 19 | \value{ 20 | return a plot if geomfunc!=Null or a list(option, mapping) if 21 | geomfunc = NULL. 22 | } 23 | \description{ 24 | A helper function used by ggpubr functions to execute any geom_* 25 | functions in ggplot2. Useful only when you want to call a geom_* function 26 | without carrying about the arguments to put in aes(). Basic users of ggpubr 27 | don't need this function. 28 | } 29 | \examples{ 30 | \dontrun{ 31 | ggplot() + geom_exec(geom_point, data = mtcars, 32 | x = "mpg", y = "wt", size = "cyl", color = "cyl") 33 | } 34 | } 35 | -------------------------------------------------------------------------------- /man/geom_signif.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils-geom-signif.R 3 | \name{geom_signif} 4 | \alias{geom_signif} 5 | \title{geom_signif exported from ggsignif package} 6 | \description{ 7 | See \code{ggsignif::\link[ggsignif:stat_signif]{geom_signif}} for details. 8 | } 9 | \keyword{internal} 10 | -------------------------------------------------------------------------------- /man/get_breaks.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/get_breaks.R 3 | \name{get_breaks} 4 | \alias{get_breaks} 5 | \title{Easy Break Creation for Numeric Axes} 6 | \usage{ 7 | get_breaks(n = NULL, by = NULL, from = NULL, to = NULL) 8 | } 9 | \arguments{ 10 | \item{n}{number of breaks.} 11 | 12 | \item{by}{number: the step between breaks.} 13 | 14 | \item{from}{the starting value of breaks. By default, 0 is used for positive 15 | variables} 16 | 17 | \item{to}{the end values of breaks. This corresponds generally to the maximum 18 | limit of the axis.} 19 | } 20 | \value{ 21 | a break function 22 | } 23 | \description{ 24 | Creates breaks for numeric axes to be used in the functions 25 | \code{\link[ggplot2:scale_continuous]{scale_x_continuous}()} and 26 | \code{\link[ggplot2:scale_continuous]{scale_y_continuous}()}. Can be used to increase the 27 | number of x and y ticks by specifying the option \code{n}. It's also 28 | possible to control axis breaks by specifying a step between ticks. For 29 | example, if \code{by = 5}, a tick mark is shown on every 5. 30 | } 31 | \examples{ 32 | 33 | # Generate 5 breaks for a variable x 34 | get_breaks(n = 5)(x = 1:100) 35 | 36 | # Generate breaks using an increasing step 37 | get_breaks(by = 10)(x = 1:100) 38 | 39 | # Combine with ggplot scale_xx functions 40 | library(ggplot2) 41 | 42 | # Create a basic plot 43 | p <- ggscatter(mtcars, x = "wt", y = "mpg") 44 | p 45 | 46 | # Increase the number of ticks 47 | p + 48 | scale_x_continuous(breaks = get_breaks(n = 10)) + 49 | scale_y_continuous(breaks = get_breaks(n = 10)) 50 | 51 | # Set ticks according to a specific step, starting from 0 52 | p + scale_x_continuous( 53 | breaks = get_breaks(by = 1.5, from = 0), 54 | limits = c(0, 6) 55 | ) + 56 | scale_y_continuous( 57 | breaks = get_breaks(by = 10, from = 0), 58 | limits = c(0, 40) 59 | ) 60 | 61 | } 62 | -------------------------------------------------------------------------------- /man/get_legend.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/get_legend.R 3 | \name{get_legend} 4 | \alias{get_legend} 5 | \title{Extract Legends from a ggplot object} 6 | \usage{ 7 | get_legend(p, position = NULL) 8 | } 9 | \arguments{ 10 | \item{p}{an object of class ggplot or a list of ggplots. If p is a list, only the first legend is returned.} 11 | 12 | \item{position}{character specifying legend position. Allowed values are one of 13 | c("top", "bottom", "left", "right", "none"). To remove the legend use 14 | legend = "none".} 15 | } 16 | \value{ 17 | an object of class gtable. 18 | } 19 | \description{ 20 | Extract the legend labels from a ggplot object. 21 | } 22 | \examples{ 23 | # Create a scatter plot 24 | p <- ggscatter(iris, x = "Sepal.Length", y = "Sepal.Width", 25 | color = "Species", palette = "jco", 26 | ggtheme = theme_minimal()) 27 | p 28 | 29 | # Extract the legend. Returns a gtable 30 | leg <- get_legend(p) 31 | 32 | # Convert to a ggplot and print 33 | as_ggplot(leg) 34 | 35 | } 36 | -------------------------------------------------------------------------------- /man/ggexport.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ggexport.R 3 | \name{ggexport} 4 | \alias{ggexport} 5 | \title{Export ggplots} 6 | \usage{ 7 | ggexport( 8 | ..., 9 | plotlist = NULL, 10 | filename = NULL, 11 | ncol = NULL, 12 | nrow = NULL, 13 | width = 480, 14 | height = 480, 15 | pointsize = 12, 16 | res = NA, 17 | verbose = TRUE 18 | ) 19 | } 20 | \arguments{ 21 | \item{...}{list of plots to be arranged into the grid. The plots can be either 22 | ggplot2 plot objects, arbitrary gtables or an object of class 23 | \code{\link{ggarrange}}.} 24 | 25 | \item{plotlist}{(optional) list of plots to display.} 26 | 27 | \item{filename}{File name to create on disk.} 28 | 29 | \item{ncol}{(optional) number of columns in the plot grid.} 30 | 31 | \item{nrow}{(optional) number of rows in the plot grid.} 32 | 33 | \item{width, height}{plot width and height, respectively (example, width = 800, 34 | height = 800). Applied only to raster plots: "png", "jpeg", "jpg", "bmp" and 35 | "tiff".} 36 | 37 | \item{pointsize}{the default pointsize of plotted text (example, pointsize = 38 | 8). Used only for raster plots.} 39 | 40 | \item{res}{the resolution in ppi (example, res = 250). Used only for raster 41 | plots.} 42 | 43 | \item{verbose}{logical. If TRUE, show message.} 44 | } 45 | \description{ 46 | Export ggplots 47 | } 48 | \examples{ 49 | \dontrun{ 50 | require("magrittr") 51 | # Load data 52 | data("ToothGrowth") 53 | df <- ToothGrowth 54 | df$dose <- as.factor(df$dose) 55 | 56 | # Box plot 57 | bxp <- ggboxplot(df, x = "dose", y = "len", 58 | color = "dose", palette = "jco") 59 | # Dot plot 60 | dp <- ggdotplot(df, x = "dose", y = "len", 61 | color = "dose", palette = "jco") 62 | # Density plot 63 | dens <- ggdensity(df, x = "len", fill = "dose", palette = "jco") 64 | 65 | # Export to pdf 66 | ggarrange(bxp, dp, dens, ncol = 2) \%>\% 67 | ggexport(filename = "test.pdf") 68 | 69 | # Export to png 70 | ggarrange(bxp, dp, dens, ncol = 2) \%>\% 71 | ggexport(filename = "test.png") 72 | } 73 | 74 | } 75 | \author{ 76 | Alboukadel Kassambara 77 | } 78 | -------------------------------------------------------------------------------- /man/ggparagraph.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ggparagraph.R 3 | \name{ggparagraph} 4 | \alias{ggparagraph} 5 | \alias{drawDetails.splitText} 6 | \title{Draw a Paragraph of Text} 7 | \usage{ 8 | ggparagraph( 9 | text, 10 | color = NULL, 11 | size = NULL, 12 | face = NULL, 13 | family = NULL, 14 | lineheight = NULL 15 | ) 16 | 17 | \method{drawDetails}{splitText}(x, recording) 18 | } 19 | \arguments{ 20 | \item{text}{the text to plot.} 21 | 22 | \item{color}{font color, example: color = "black"} 23 | 24 | \item{size}{font size, example: size = 12} 25 | 26 | \item{face}{font face. Allowed values are one of "plain", "italic", "bold", 27 | "bold.italic".} 28 | 29 | \item{family}{font family} 30 | 31 | \item{lineheight}{Line height, example: lineheight = 2.} 32 | 33 | \item{x}{a grid grob} 34 | 35 | \item{recording}{a logical value indicating whether a grob is being added to 36 | the display list or redrawn from the display list.} 37 | } 38 | \description{ 39 | Draw a paragraph o text. Splits a long text into multiple lines 40 | (by inserting line breaks) so that the output will fit within the current 41 | viewport. 42 | } 43 | \examples{ 44 | # Density plot 45 | density.p <- ggdensity(iris, x = "Sepal.Length", 46 | fill = "Species", palette = "jco") 47 | 48 | # Text plot 49 | text <- paste("iris data set gives the measurements in cm", 50 | "of the variables sepal length and width", 51 | "and petal length and width, respectively,", 52 | "for 50 flowers from each of 3 species of iris.", 53 | "The species are Iris setosa, versicolor, and virginica.", sep = " ") 54 | text.p <- ggparagraph(text, face = "italic", size = 12) 55 | 56 | # Arrange the plots on the same page 57 | ggarrange(density.p, text.p, 58 | ncol = 1, nrow = 2, 59 | heights = c(1, 0.3)) 60 | 61 | } 62 | \author{ 63 | Alboukadel Kassambara 64 | } 65 | -------------------------------------------------------------------------------- /man/ggpubr-package.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ggpubr-package.R 3 | \docType{package} 4 | \name{ggpubr-package} 5 | \alias{ggpubr} 6 | \alias{ggpubr-package} 7 | \title{ggpubr: 'ggplot2' Based Publication Ready Plots} 8 | \description{ 9 | The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots. 10 | } 11 | \details{ 12 | General resources: 13 | 14 | \itemize{ 15 | \item \href{https://rpkgs.datanovia.com/ggpubr/}{ggpubr documentation} 16 | \item \href{https://www.datanovia.com/en/blog/tag/ggpubr/}{ggpubr tutorials} 17 | } 18 | } 19 | \section{Package options}{ 20 | 21 | 22 | \describe{ 23 | \item{ggpubr.parse_aes}{logical indicating whether to parse or not aesthetics variables names. 24 | Default is \code{TRUE}. For example, if you want \code{ggpubr} to handle non-standard column names, like \code{A-A}, 25 | without parsing, then set this option to \code{FALSE} using \code{options(ggpubr.parse_aes = FALSE)}.} 26 | \item{ggpubr.null_device}{A function that creates an appropriate null device. 27 | These include: \code{\link[cowplot:pdf_null_device]{cowplot::pdf_null_device}}, 28 | \code{\link[cowplot:png_null_device]{cowplot::png_null_device}}, 29 | \code{\link[cowplot:cairo_null_device]{cowplot::cairo_null_device}} and 30 | \code{\link[cowplot:agg_null_device]{cowplot::agg_null_device}}. Default is 31 | \code{\link[cowplot:pdf_null_device]{cowplot::pdf_null_device}}. This is used in 32 | function like \code{\link{as_ggplot}()}, which needs to open a graphics 33 | device to render ggplot objects into grid graphics objects. This function is 34 | used to open null device for avoiding the display of unnecessary blank page 35 | when calling \code{\link{ggarrange}()} or \code{\link{as_ggplot}()}} } 36 | } 37 | 38 | \seealso{ 39 | Useful links: 40 | \itemize{ 41 | \item \url{https://rpkgs.datanovia.com/ggpubr/} 42 | \item Report bugs at \url{https://github.com/kassambara/ggpubr/issues} 43 | } 44 | 45 | } 46 | \author{ 47 | \strong{Maintainer}: Alboukadel Kassambara \email{alboukadel.kassambara@gmail.com} 48 | 49 | } 50 | \keyword{internal} 51 | -------------------------------------------------------------------------------- /man/ggpubr_options.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ggpubr_options.R 3 | \name{ggpubr_options} 4 | \alias{ggpubr_options} 5 | \title{Global Options for GGPubr} 6 | \usage{ 7 | ggpubr_options() 8 | } 9 | \description{ 10 | Displays allowed global options in ggpubr. 11 | } 12 | \examples{ 13 | 14 | ggpubr_options() 15 | 16 | } 17 | -------------------------------------------------------------------------------- /man/gradient_color.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/gradient_color.R 3 | \name{gradient_color} 4 | \alias{gradient_color} 5 | \alias{gradient_fill} 6 | \title{Set Gradient Color} 7 | \usage{ 8 | gradient_color(palette) 9 | 10 | gradient_fill(palette) 11 | } 12 | \arguments{ 13 | \item{palette}{the color palette to be used for coloring or filling by 14 | groups. Allowed values include "grey" for grey color palettes; brewer 15 | palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", 16 | "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", 17 | "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and 18 | "rickandmorty". Can be also a numeric vector; in this 19 | case a basic color palette is created using the function 20 | \link[grDevices]{palette}.} 21 | } 22 | \description{ 23 | Change gradient color. 24 | \itemize{ 25 | \item \code{gradient_color()}: Change gradient color. 26 | \item \code{gradient_fill()}: Change gradient fill. 27 | } 28 | } 29 | \examples{ 30 | df <- mtcars 31 | p <- ggscatter(df, x = "wt", y = "mpg", 32 | color = "mpg") 33 | 34 | # Change gradient color 35 | # Use one custom color 36 | p + gradient_color("red") 37 | 38 | # Two colors 39 | p + gradient_color(c("blue", "red")) 40 | 41 | # Three colors 42 | p + gradient_color(c("blue", "white", "red")) 43 | 44 | # Use RColorBrewer palette 45 | p + gradient_color("RdYlBu") 46 | 47 | # Use ggsci color palette 48 | p + gradient_color("npg") 49 | } 50 | \seealso{ 51 | \link{set_palette}. 52 | } 53 | -------------------------------------------------------------------------------- /man/grids.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/grids.R 3 | \name{grids} 4 | \alias{grids} 5 | \title{Add Grids to a ggplot} 6 | \usage{ 7 | grids(axis = c("xy", "x", "y"), color = "grey92", size = NULL, linetype = NULL) 8 | } 9 | \arguments{ 10 | \item{axis}{axis for which grid should be added. Allowed values include \code{c("xy", "x", "y")}.} 11 | 12 | \item{color}{grid line color.} 13 | 14 | \item{size}{numeric value specifying grid line size.} 15 | 16 | \item{linetype}{line type. An integer (0:8), a name (blank, solid, dashed, 17 | dotted, dotdash, longdash, twodash). Sess \code{\link{show_line_types}}.} 18 | } 19 | \description{ 20 | Add grids to ggplot. 21 | } 22 | \examples{ 23 | # Load data 24 | data("ToothGrowth") 25 | 26 | # Basic plot 27 | p <- ggboxplot(ToothGrowth, x = "dose", y = "len") 28 | p 29 | 30 | # Add border 31 | p + grids(linetype = "dashed") 32 | } 33 | -------------------------------------------------------------------------------- /man/npc_to_data_coord.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/npc_to_data_coord.R 3 | \name{npc_to_data_coord} 4 | \alias{npc_to_data_coord} 5 | \title{Convert NPC to Data Coordinates} 6 | \usage{ 7 | npc_to_data_coord(npc, data.ranges) 8 | } 9 | \arguments{ 10 | \item{npc}{a numeric vector. Each value should be in [0-1]} 11 | 12 | \item{data.ranges}{a numeric vector of length 2 containing the data ranges (minimum and the maximum)} 13 | } 14 | \value{ 15 | a numeric vector representing data coordinates. 16 | } 17 | \description{ 18 | Convert NPC (Normalized Parent Coordinates) into data coordinates. 19 | } 20 | \examples{ 21 | npc_to_data_coord(npc = c(0.2, 0.95), data.ranges = c(1, 20)) 22 | as_npc(c("top", "right")) \%>\% 23 | npc_to_data_coord(data.ranges = c(1, 20)) 24 | 25 | } 26 | \seealso{ 27 | \code{\link{as_npc}}, \code{\link{get_coord}}. 28 | } 29 | -------------------------------------------------------------------------------- /man/pipe.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/utils-pipe.R 3 | \name{\%>\%} 4 | \alias{\%>\%} 5 | \title{Pipe operator} 6 | \usage{ 7 | lhs \%>\% rhs 8 | } 9 | \description{ 10 | See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details. 11 | } 12 | \keyword{internal} 13 | -------------------------------------------------------------------------------- /man/reexports.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/reexports.R 3 | \docType{import} 4 | \name{reexports} 5 | \alias{reexports} 6 | \alias{mutate} 7 | \alias{group_by} 8 | \alias{get_summary_stats} 9 | \title{Objects exported from other packages} 10 | \keyword{internal} 11 | \description{ 12 | These objects are imported from other packages. Follow the links 13 | below to see their documentation. 14 | 15 | \describe{ 16 | \item{dplyr}{\code{\link[dplyr]{group_by}}, \code{\link[dplyr]{mutate}}} 17 | 18 | \item{rstatix}{\code{\link[rstatix]{get_summary_stats}}} 19 | }} 20 | 21 | -------------------------------------------------------------------------------- /man/rotate.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/rotate.R 3 | \name{rotate} 4 | \alias{rotate} 5 | \title{Rotate a ggplot Horizontally} 6 | \usage{ 7 | rotate(...) 8 | } 9 | \arguments{ 10 | \item{...}{other arguments to pass to \code{\link[ggplot2]{coord_flip}}.} 11 | } 12 | \description{ 13 | Rotate a ggplot to create horizontal plots. Wrapper around 14 | \code{\link[ggplot2]{coord_flip}}. 15 | } 16 | \examples{ 17 | # Load data 18 | data("ToothGrowth") 19 | df <- ToothGrowth 20 | 21 | # Basic plot 22 | p <- ggboxplot(df, x = "dose", y = "len", 23 | color = "dose", palette = "jco") 24 | p 25 | # Create horizontal plots 26 | p + rotate() 27 | } 28 | -------------------------------------------------------------------------------- /man/rotate_axis_text.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/rotate_axis_text.R 3 | \name{rotate_axis_text} 4 | \alias{rotate_axis_text} 5 | \alias{rotate_x_text} 6 | \alias{rotate_y_text} 7 | \title{Rotate Axes Text} 8 | \usage{ 9 | rotate_x_text(angle = 90, hjust = NULL, vjust = NULL, ...) 10 | 11 | rotate_y_text(angle = 90, hjust = NULL, vjust = NULL, ...) 12 | } 13 | \arguments{ 14 | \item{angle}{numeric value specifying the rotation angle. Default is 90 for vertical x-axis text.} 15 | 16 | \item{hjust}{horizontal justification (in [0, 1]).} 17 | 18 | \item{vjust}{vertical justification (in [0, 1]).} 19 | 20 | \item{...}{other arguments to pass to the function 21 | \code{\link[ggplot2:element]{element_text}()}.} 22 | } 23 | \description{ 24 | Rotate the x-axis text (tick mark labels). 25 | \itemize{ 26 | \item \code{rotate_x_text}(): Rotate x axis text. 27 | \item \code{rotate_y_text}(): Rotate y axis text. 28 | } 29 | } 30 | \examples{ 31 | # Load data 32 | data("ToothGrowth") 33 | df <- ToothGrowth 34 | 35 | # Basic plot 36 | p <- ggboxplot(df, x = "dose", y = "len") 37 | p 38 | # Vertical x axis text 39 | p + rotate_x_text() 40 | # Set rotation angle to 45 41 | p + rotate_x_text(45) 42 | p + rotate_y_text(45) 43 | 44 | } 45 | -------------------------------------------------------------------------------- /man/rremove.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/rremove.R 3 | \name{rremove} 4 | \alias{rremove} 5 | \title{Remove a ggplot Component} 6 | \usage{ 7 | rremove(object) 8 | } 9 | \arguments{ 10 | \item{object}{character string specifying the plot components. Allowed values 11 | include: \itemize{ 12 | \item \code{"grid"} for both x and y grids 13 | \item \code{"x.grid"} for x axis grids 14 | \item \code{"y.grid"} for y axis grids 15 | \item \code{"axis"} for both x and y axes 16 | \item \code{"x.axis"} for x axis 17 | \item \code{"y.axis"} for y axis 18 | 19 | \item \code{"xlab", or "x.title"} 20 | for x axis label 21 | \item \code{"ylab", or "y.title"} for y axis label 22 | \item \code{"xylab", "xy.title" or "axis.title"} for both x and y axis 23 | labels 24 | \item \code{"x.text"} for x axis texts (x axis tick labels) 25 | \item \code{"y.text"} for y axis texts (y axis tick labels) 26 | \item \code{"xy.text"} or \code{"axis.text"} for both x and y axis texts 27 | 28 | \item \code{"ticks"} for both x and y ticks 29 | \item \code{"x.ticks"} for x ticks 30 | \item \code{"y.ticks"} for y ticks 31 | 32 | \item \code{"legend.title"} for the legend title 33 | \item \code{"legend"} for the legend 34 | }} 35 | } 36 | \description{ 37 | Remove a specific component from a ggplot. 38 | } 39 | \examples{ 40 | # Load data 41 | data("ToothGrowth") 42 | 43 | # Basic plot 44 | p <- ggboxplot(ToothGrowth, x = "dose", y = "len", 45 | ggtheme = theme_gray()) 46 | p 47 | 48 | # Remove all grids 49 | p + rremove("grid") 50 | 51 | # Remove only x grids 52 | p + rremove("x.grid") 53 | } 54 | -------------------------------------------------------------------------------- /man/set_palette.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/set_palette.R 3 | \name{set_palette} 4 | \alias{set_palette} 5 | \alias{change_palette} 6 | \alias{color_palette} 7 | \alias{fill_palette} 8 | \title{Set Color Palette} 9 | \usage{ 10 | set_palette(p, palette) 11 | 12 | change_palette(p, palette) 13 | 14 | color_palette(palette = NULL, ...) 15 | 16 | fill_palette(palette = NULL, ...) 17 | } 18 | \arguments{ 19 | \item{p}{a ggplot} 20 | 21 | \item{palette}{Color palette. Allowed values include: \itemize{ \item 22 | \strong{Grey color palettes}: "grey" or "gray"; \item \strong{RColorBrewer 23 | palettes}, see \code{\link[RColorBrewer:ColorBrewer]{brewer.pal}} and details section. 24 | Examples of palette names include: "RdBu", "Blues", "Dark2", "Set2", ...; 25 | \item \strong{Custom color palettes}. For example, palette = c("#00AFBB", 26 | "#E7B800", "#FC4E07"); \item \strong{ggsci scientific journal palettes}, 27 | e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and 28 | "rickandmorty". }} 29 | 30 | \item{...}{other arguments passed to ggplot2 scale_color_xxx() and 31 | scale_fill_xxx() functions.} 32 | } 33 | \description{ 34 | \itemize{ \item \code{change_palette(), set_palette()}: Change 35 | both color and fill palettes. \item \code{color_palette()}: change color 36 | palette only. \item \code{fill_palette()}: change fill palette only. 37 | 38 | } 39 | } 40 | \examples{ 41 | # Load data 42 | data("ToothGrowth") 43 | df <- ToothGrowth 44 | 45 | # Basic plot 46 | p <- ggboxplot(df, x = "dose", y = "len", 47 | color = "dose") 48 | p 49 | 50 | # Change the color palette 51 | set_palette(p, "jco") 52 | } 53 | \seealso{ 54 | \link{get_palette}. 55 | } 56 | -------------------------------------------------------------------------------- /man/show_line_types.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/show_line_types.R 3 | \name{show_line_types} 4 | \alias{show_line_types} 5 | \title{Line types available in R} 6 | \usage{ 7 | show_line_types() 8 | } 9 | \value{ 10 | a ggplot. 11 | } 12 | \description{ 13 | Show line types available in R. 14 | } 15 | \examples{ 16 | show_line_types()+ 17 | theme_minimal() 18 | } 19 | \seealso{ 20 | \code{\link{ggpar}} and \code{\link{ggline}}. 21 | } 22 | -------------------------------------------------------------------------------- /man/show_point_shapes.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/show_point_shapes.R 3 | \name{show_point_shapes} 4 | \alias{show_point_shapes} 5 | \title{Point shapes available in R} 6 | \usage{ 7 | show_point_shapes() 8 | } 9 | \value{ 10 | a ggplot. 11 | } 12 | \description{ 13 | Show point shapes available in R. 14 | } 15 | \examples{ 16 | show_point_shapes()+ 17 | theme_minimal() 18 | } 19 | \seealso{ 20 | \code{\link{ggpar}} and \code{\link{ggline}}. 21 | } 22 | -------------------------------------------------------------------------------- /man/text_grob.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/text_grob.R 3 | \name{text_grob} 4 | \alias{text_grob} 5 | \title{Create a Text Graphical object} 6 | \usage{ 7 | text_grob( 8 | label, 9 | just = "centre", 10 | hjust = NULL, 11 | vjust = NULL, 12 | rot = 0, 13 | color = "black", 14 | face = "plain", 15 | size = NULL, 16 | lineheight = NULL, 17 | family = NULL, 18 | ... 19 | ) 20 | } 21 | \arguments{ 22 | \item{label}{A character or \link{expression} vector. Other 23 | objects are coerced by \code{\link{as.graphicsAnnot}}.} 24 | 25 | \item{just}{The justification of the text 26 | relative to its (x, y) location. If there are two values, the first 27 | value specifies horizontal justification and the second value specifies 28 | vertical justification. Possible string values are: \code{"left"}, 29 | \code{"right"}, \code{"centre"}, \code{"center"}, \code{"bottom"}, 30 | and \code{"top"}. For numeric values, 0 means left (bottom) alignment 31 | and 1 means right (top) alignment. 32 | } 33 | 34 | \item{hjust}{A numeric vector specifying horizontal justification. 35 | If specified, overrides the \code{just} setting.} 36 | 37 | \item{vjust}{A numeric vector specifying vertical justification. 38 | If specified, overrides the \code{just} setting.} 39 | 40 | \item{rot}{The angle to rotate the text.} 41 | 42 | \item{color}{text font color.} 43 | 44 | \item{face}{font face. Allowed values include one of \code{"plain", "bold", 45 | "italic", "bold.italic"}.} 46 | 47 | \item{size}{font size (e.g.: size = 12)} 48 | 49 | \item{lineheight}{line height (e.g.: lineheight = 2).} 50 | 51 | \item{family}{font family.} 52 | 53 | \item{...}{other arguments passed to \link[grid:grid.text]{textGrob}.} 54 | } 55 | \value{ 56 | a text grob. 57 | } 58 | \description{ 59 | Create easily a customized text grob (graphical object). Wrapper around 60 | \code{\link[grid:grid.text]{textGrob}}. 61 | } 62 | \examples{ 63 | text <- paste("iris data set gives the measurements in cm", 64 | "of the variables sepal length and width", 65 | "and petal length and width, respectively,", 66 | "for 50 flowers from each of 3 species of iris.", 67 | "The species are Iris setosa, versicolor, and virginica.", sep = "\n") 68 | 69 | # Create a text grob 70 | tgrob <- text_grob(text, face = "italic", color = "steelblue") 71 | # Draw the text 72 | as_ggplot(tgrob) 73 | 74 | } 75 | -------------------------------------------------------------------------------- /man/theme_transparent.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/theme_transparent.R 3 | \name{theme_transparent} 4 | \alias{theme_transparent} 5 | \title{Create a ggplot with Transparent Background} 6 | \usage{ 7 | theme_transparent(base_size = 12, base_family = "") 8 | } 9 | \arguments{ 10 | \item{base_size}{base font size} 11 | 12 | \item{base_family}{base font family} 13 | } 14 | \description{ 15 | Create a ggplot with transparent background. 16 | } 17 | \examples{ 18 | # Create a scatter plot 19 | sp <- ggscatter(iris, x = "Sepal.Length", y = "Sepal.Width", 20 | color = "Species", palette = "jco", 21 | size = 3, alpha = 0.6) 22 | sp 23 | 24 | # Transparent theme 25 | sp + theme_transparent() 26 | 27 | } 28 | \seealso{ 29 | \code{\link{theme_pubr}} 30 | } 31 | -------------------------------------------------------------------------------- /pkgdown/extra.js: -------------------------------------------------------------------------------- 1 | /* Analytics */ 2 | function loadGoogleAnalytics(){ 3 | var ga = document.createElement('script'); 4 | ga.type = 'text/javascript'; 5 | ga.async = true; 6 | ga.src = 'https://www.googletagmanager.com/gtag/js?id=UA-54921687-5'; 7 | 8 | var s = document.getElementsByTagName('script')[0]; 9 | s.parentNode.insertBefore(ga, s); 10 | } 11 | loadGoogleAnalytics(); //Create the script 12 | window.dataLayer = window.dataLayer || []; 13 | function gtag(){dataLayer.push(arguments);} 14 | gtag('js', new Date()); 15 | gtag('config', 'UA-54921687-5'); 16 | -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- 1 | library(testthat) 2 | library(ggpubr) 3 | 4 | test_check("ggpubr") 5 | -------------------------------------------------------------------------------- /tests/testthat/test-as_npc.R: -------------------------------------------------------------------------------- 1 | context("test-as_npc") 2 | 3 | test_that("as_npc returns the same value as the input when the input is.numeric", { 4 | expect_equal(as_npc(0.5), 0.5) 5 | }) 6 | 7 | 8 | test_that("as_npc works correctly for character coordinates", { 9 | res <- as_npc(c('right', 'left', 'bottom', 'top', 'center', 'centre', 'middle')) 10 | expect_equal(res, c(0.95, 0.05, 0.05, 0.95, 0.5, 0.5, 0.5)) 11 | }) 12 | -------------------------------------------------------------------------------- /tests/testthat/test-create_aes.R: -------------------------------------------------------------------------------- 1 | context("test-create_aes") 2 | 3 | test_that("parse_expression works for a valid variable name", { 4 | observed <- parse_expression("a") 5 | expected <- parse(text = "a")[[1]] 6 | expect_equal(observed, expected) 7 | }) 8 | 9 | 10 | test_that("parse_expression works for a variable name containing space", { 11 | observed <- parse_expression("a b") 12 | expected <- as.name("a b") 13 | expect_equal(observed, expected) 14 | }) 15 | 16 | test_that("parse_expression works for a mathetical expression", { 17 | observed <- parse_expression("log2( a + b )") 18 | expected <- parse(text = "log2( a + b )")[[1]] 19 | expect_equal(observed, expected) 20 | }) 21 | 22 | -------------------------------------------------------------------------------- /tests/testthat/test-facet.R: -------------------------------------------------------------------------------- 1 | 2 | # Data preparation 3 | data("ToothGrowth") 4 | df <- ToothGrowth 5 | # Adding column name with space 6 | df[['spa ced']] <- df[['supp']] 7 | 8 | 9 | test_that("facet works", { 10 | p <- ggpubr::ggboxplot(df, "dose", "len", facet.by = "supp") 11 | panels <- ggplot2::layer_data(p)[["PANEL"]] %>% 12 | unique() %>% 13 | as.numeric() 14 | expect_equal(panels, c(1, 2)) 15 | }) 16 | 17 | 18 | test_that("facet works when column names contain space", { 19 | p <- ggpubr::ggboxplot(df, "dose", "len", facet.by = "spa ced") 20 | panels <- ggplot2::layer_data(p)[["PANEL"]] %>% 21 | unique() %>% 22 | as.numeric() 23 | expect_equal(panels, c(1, 2)) 24 | }) 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /tests/testthat/test-get_coord.R: -------------------------------------------------------------------------------- 1 | context("test-get_coord") 2 | 3 | # Basic plots: one group ----------------------------------- 4 | test_that("No transformation is performed when coord specified", { 5 | res_10 <- get_coord(coord = 10) 6 | res_text <- get_coord(coord = "text") 7 | expect_equal(res_10, 10) 8 | expect_equal(res_text, "text") 9 | }) 10 | 11 | test_that("get_coord works for one group", { 12 | # x- axis 13 | res_left <- get_coord( 14 | data.ranges = c(1, 3), group = 1, 15 | npc = "left", step = 0.1, margin.npc = 0 16 | ) 17 | # Y -axis 18 | res_top<- get_coord( 19 | data.ranges = c(4.2, 36.4), group = 1, 20 | npc = "top", step = -0.1, margin.npc = 0 21 | ) 22 | expect_equal(res_top, 36.4) 23 | }) 24 | 25 | 26 | # Grouped plots -------------------------- 27 | test_that("get_coord works for grouped plots", { 28 | # x- axis 29 | res_left <- get_coord( 30 | data.ranges = c(1, 3), group = 1:3, 31 | npc = "left", step = 0.1, margin.npc = 0 32 | ) 33 | # no transformation when coord specified 34 | res_coord <- get_coord( 35 | data.ranges = c(1, 3), group = 1:3, 36 | coord = 1:3, step = 0.1, margin.npc = 0 37 | ) 38 | # Y-axis 39 | res_top <- get_coord( 40 | data.ranges = c(4.2, 36.4), group = c(1, 2, 3), 41 | npc = "top", step = -0.1, margin.npc = 0 42 | ) 43 | expect_equal(res_left, c(1.0, 1.2, 1.4)) 44 | expect_equal(res_coord, 1:3) 45 | expect_equal(res_top, c(36.40, 39.62, 42.84)) 46 | }) 47 | 48 | -------------------------------------------------------------------------------- /tests/testthat/test-ggadjust_pvalue.R: -------------------------------------------------------------------------------- 1 | # Data preparation 2 | #::::::::::::::::::::::::::::::::::::::: 3 | df <- ToothGrowth 4 | df$dose <- as.factor(df$dose) 5 | # Add a random grouping variable 6 | df$group <- factor(rep(c("grp1", "grp2"), 30)) 7 | 8 | 9 | test_that("ggadjust_pvalue works for geom_pwc() pairwise comparison using facet", { 10 | p <- ggboxplot(df, x = "supp", y = "len", facet.by = "dose") + 11 | geom_pwc(method = "t_test") 12 | # Adjust all p-values together after 13 | stat_test <- ggadjust_pvalue( 14 | p, p.adjust.method = "bonferroni", 15 | label = "{p.adj.format}{p.adj.signif}", 16 | output = "stat_test" 17 | ) 18 | stat_test <- stat_test %>% 19 | dplyr::select(PANEL, x, y, group, group1, group2, label) %>% 20 | mutate(x = as.numeric(x), label = as.character(label)) 21 | expected <- tibble::tribble( 22 | ~PANEL, ~x, ~y, ~group, ~group1, ~group2, ~label, 23 | "1", 1, 34.494, 1, "1", "2", "0.0191*", 24 | "1", 1, 35.385, 1, "1", "2", "0.0191*", 25 | "1", 2, 35.385, 1, "1", "2", "0.0191*", 26 | "2", 1, 34.494, 1, "1", "2", "0.0031**", 27 | "2", 1, 35.385, 1, "1", "2", "0.0031**", 28 | "2", 2, 35.385, 1, "1", "2", "0.0031**", 29 | "3", 1, 34.494, 1, "1", "2", "1ns", 30 | "3", 1, 35.385, 1, "1", "2", "1ns", 31 | "3", 2, 35.385, 1, "1", "2", "1ns" 32 | ) %>% 33 | dplyr::mutate(PANEL = as.factor(PANEL)) %>% 34 | as.data.frame(stringAsFactor = FALSE) 35 | expect_equal(stat_test, expected) 36 | }) 37 | -------------------------------------------------------------------------------- /tests/testthat/test-ggboxplot.R: -------------------------------------------------------------------------------- 1 | 2 | test_that("The position of jittered points is reproducible in ggboxplot", { 3 | p <- ggboxplot(PlantGrowth, x = "group", y = "weight", add = "jitter") 4 | jitter_data <- layer_data(p, 2) %>% 5 | dplyr::select(x, y) %>% 6 | dplyr::mutate(x = as.numeric(round(x, 7)), y = as.numeric(round(y, 7))) 7 | expected_data <-tibble::tribble( 8 | ~x, ~y, 9 | 0.915031, 4.1737042, 10 | 1.1153221, 5.5832184, 11 | 0.9635908, 5.1815256, 12 | 1.153207, 6.1123637, 13 | 1.1761869, 4.4961969, 14 | 0.8182226, 4.6098224, 15 | 1.0112422, 5.1720677, 16 | 1.1569676, 4.5277313, 17 | 1.020574, 5.3285454, 18 | 0.9826459, 5.137853, 19 | 2.1827333, 4.8071424, 20 | 1.9813337, 4.1693164, 21 | 2.0710283, 4.4093098, 22 | 2.0290534, 3.5889508, 23 | 1.8411699, 5.8672196, 24 | 2.15993, 3.8271104, 25 | 1.8984351, 6.0278643, 26 | 1.8168238, 4.8897277, 27 | 1.9311683, 4.3181278, 28 | 2.1818015, 4.6928626, 29 | 3.1558157, 6.3063666, 30 | 3.0771214, 5.1195376, 31 | 3.0562027, 5.5423914, 32 | 3.1977079, 5.4969752, 33 | 3.0622823, 5.3704876, 34 | 3.0834122, 5.2876523, 35 | 3.0176264, 4.9170203, 36 | 3.0376568, 6.1520265, 37 | 2.9156639, 5.8031604, 38 | 2.8588455, 5.2589957 39 | ) %>% 40 | as.data.frame() 41 | expect_equal(jitter_data, expected_data) 42 | }) 43 | 44 | 45 | 46 | 47 | 48 | 49 | -------------------------------------------------------------------------------- /tests/testthat/test-gghistogram.R: -------------------------------------------------------------------------------- 1 | context("gghistogram") 2 | 3 | test_that("gghistogram works when using after_stat()", { 4 | p <- gghistogram(iris, x = "Sepal.Length", y = "after_stat(density * width)", bins = 30) 5 | p_build <- ggplot2::ggplot_build(p) 6 | df <- p_build$data[[1]] 7 | observed_count <- df$count 8 | expected_count <- c(4, 1, 4, 2, 11, 10, 9, 4, 7, 7, 6, 8, 7, 9, 6, 4, 9, 12, 2, 8, 3, 5, 1, 3, 1, 1, 1, 4, 0, 1) 9 | expect_equal(observed_count, expected_count) 10 | }) 11 | 12 | 13 | test_that("gghistogram works when using after_stat() with trailing space inside parentheses", { 14 | p <- gghistogram(iris, x = "Sepal.Length", y = "after_stat(density )", bins = 30) 15 | p_build <- ggplot2::ggplot_build(p) 16 | df <- p_build$data[[1]] 17 | observed_count <- df$count 18 | expected_count <- c(4, 1, 4, 2, 11, 10, 9, 4, 7, 7, 6, 8, 7, 9, 6, 4, 9, 12, 2, 8, 3, 5, 1, 3, 1, 1, 1, 4, 0, 1) 19 | expect_equal(observed_count, expected_count) 20 | }) 21 | -------------------------------------------------------------------------------- /tests/testthat/test-ggscatter.R: -------------------------------------------------------------------------------- 1 | context("ggscatter") 2 | 3 | test_that("ggscatter works when there is spaces in variable names", { 4 | data("mtcars") 5 | df <- mtcars[, c("wt", "mpg")] 6 | colnames(df) <- c("Dimension 1", "Dimension 2") 7 | p <- ggscatter(df, x = "Dimension 1", y = "Dimension 2" ) 8 | p_build <- ggplot2::ggplot_build(p) 9 | df_build <- p_build$data[[1]] 10 | expect_equal(df$`Dimension 1`, df_build$x) 11 | }) 12 | 13 | 14 | test_that("ggscatter can handle non-standard column names when ggpubr.parse_aes global option is set to FALSE (#229)", { 15 | data("mtcars") 16 | df <- mtcars[, c("wt", "mpg")] 17 | colnames(df) <- c("A-A", "B-B") 18 | 19 | old_options <- options(ggpubr.parse_aes = FALSE) 20 | p <- ggscatter(df, x = "A-A", y = "B-B" ) 21 | options(old_options) 22 | p_build <- ggplot2::ggplot_build(p) 23 | df_build <- p_build$data[[1]] 24 | expect_equal(df$`A-A`, df_build$x) 25 | }) 26 | -------------------------------------------------------------------------------- /tests/testthat/test-ggstripchart.R: -------------------------------------------------------------------------------- 1 | 2 | test_that("ggstripchart is reproducible", { 3 | p <- ggstripchart(PlantGrowth, x = "group", y = "weight") 4 | jitter_data <- layer_data(p, 1) %>% 5 | dplyr::select(x, y) %>% 6 | dplyr::mutate(x = as.numeric(round(x, 7)), y = as.numeric(round(y, 7))) 7 | expected_data <- data.frame( 8 | x = c(0.915031,1.1153221,0.9635908, 9 | 1.153207,1.1761869,0.8182226,1.0112422,1.1569676,1.020574, 10 | 0.9826459,2.1827333,1.9813337,2.0710283,2.0290534, 11 | 1.8411699,2.15993,1.8984351,1.8168238,1.9311683,2.1818015, 12 | 3.1558157,3.0771214,3.0562027,3.1977079,3.0622823, 13 | 3.0834122,3.0176264,3.0376568,2.9156639,2.8588455), 14 | y = c(4.1737042,5.5832184,5.1815256, 15 | 6.1123637,4.4961969,4.6098224,5.1720677,4.5277313,5.3285454, 16 | 5.137853,4.8071424,4.1693164,4.4093098,3.5889508, 17 | 5.8672196,3.8271104,6.0278643,4.8897277,4.3181278,4.6928626, 18 | 6.3063666,5.1195376,5.5423914,5.4969752,5.3704876, 19 | 5.2876523,4.9170203,6.1520265,5.8031604,5.2589957) 20 | ) 21 | expect_equal(jitter_data, expected_data) 22 | }) 23 | 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /tests/testthat/test-ggtext.R: -------------------------------------------------------------------------------- 1 | data("gene_expression", package = "ggpubr") 2 | 3 | test_that(".get_label_data works when label.select specified as a list", { 4 | results <- .get_label_data( 5 | data = gene_expression, x = "dataset", y = "XBP1", label ="bcr_patient_barcode", 6 | label.select = list(criteria = "`y` > 4.4 & `x` %in% c('BRCA', 'OV')"), 7 | ) 8 | expected <- tibble::tribble( 9 | ~bcr_patient_barcode, ~dataset, ~GATA3, ~PTEN, ~XBP1, 10 | "BRCA149", "BRCA", 2.345125, 1.13357142857143, 4.48758333333333, 11 | "BRCA536", "BRCA", 3.1135, 0.846142857142857, 4.73675, 12 | "BRCA581", "BRCA", 3.38675, 0.152928571428571, 4.5725 13 | ) %>% 14 | data.frame(stringsAsFactors = FALSE) 15 | expect_equal(results, expected, tolerance = 1e-4) 16 | }) 17 | -------------------------------------------------------------------------------- /tests/testthat/test-stat_friedman_test.R: -------------------------------------------------------------------------------- 1 | context("test-stat_friedman_test") 2 | 3 | # Data preparation 4 | df <- ToothGrowth 5 | df$dose <- as.factor(df$dose) 6 | df$id <- rep(1:10, 6) # Add individuals id 7 | # Add a random grouping variable 8 | set.seed(123) 9 | df$group <- sample(factor(rep(c("grp1", "grp2", "grp3"), 20))) 10 | df <- df %>% mutate( 11 | len = ifelse(group == "grp2", len+2, len), 12 | len = ifelse(group == "grp3", len+7, len) 13 | ) 14 | 15 | 16 | # Basic plots---------------------- 17 | test_that("stat_friedman_test works for basic plots", { 18 | df$id <- as.factor(c(rep(1:10, 3), rep(11:20, 3))) 19 | bxp <- ggboxplot(df, x = "dose", y = "len") + 20 | stat_friedman_test(wid = "id") 21 | bxp_build <- ggplot2::ggplot_build(bxp) 22 | stat.test <- bxp_build$data[[2]] 23 | expect_equal(as.numeric(stat.test$x), 1) 24 | expect_equal(as.numeric(stat.test$y), 36.4) 25 | expect_equal(stat.test$label, "Friedman test, p < 0.0001") 26 | }) 27 | 28 | 29 | test_that("stat_friedman_test works for grouped plot: group by x var", { 30 | df$id <- as.factor(rep(1:10, 6)) 31 | bxp <- ggboxplot(df, x = "dose", y = "len", color = "supp", palette = "jco") + 32 | stat_friedman_test(aes(group = supp, color = supp), 33 | label = "p.format", wid = "id", group.by = "x.var") 34 | bxp_build <- ggplot2::ggplot_build(bxp) 35 | stat.test <- bxp_build$data[[2]] 36 | # Replace possible "1." (with trailing dot) by "1" 37 | # this trailing dot appear only on linux 38 | stat.test$label <- gsub(pattern = "^1\\.$", replacement = "1", stat.test$label) 39 | expect_equal(as.numeric(stat.test$x), c(1, 2, 3)) 40 | expect_equal(as.numeric(stat.test$y), c(36.4, 36.4, 36.4)) 41 | expect_equal(stat.test$label, c("0.011", "0.058", "1")) 42 | }) 43 | 44 | test_that("stat_friedman_test works for grouped one-way repeated measure anova: group by legend var", { 45 | df$id <- as.factor(rep(1:10, 6)) 46 | bxp <- ggboxplot(df, x = "dose", y = "len", color = "supp", palette = "jco") + 47 | stat_friedman_test(aes(group = supp, color = supp), 48 | wid = "id", group.by = "legend.var") 49 | bxp_build <- ggplot2::ggplot_build(bxp) 50 | stat.test <- bxp_build$data[[2]] 51 | expect_equal(as.numeric(stat.test$x), c(0.8, 0.8)) 52 | expect_equal(as.numeric(stat.test$y), c(36.40, 39.62)) 53 | expect_equal(stat.test$label, c("Friedman test, p = 0.02472", "Friedman test, p = 0.00012")) 54 | }) 55 | -------------------------------------------------------------------------------- /tests/testthat/test-stat_kruskal_test.R: -------------------------------------------------------------------------------- 1 | context("test-stat_kruskal_test") 2 | 3 | # Data preparation 4 | df <- ToothGrowth 5 | df$dose <- as.factor(df$dose) 6 | df$id <- rep(1:10, 6) # Add individuals id 7 | # Add a random grouping variable 8 | set.seed(123) 9 | df$group <- sample(factor(rep(c("grp1", "grp2", "grp3"), 20))) 10 | df <- df %>% mutate( 11 | len = ifelse(group == "grp2", len+2, len), 12 | len = ifelse(group == "grp3", len+7, len) 13 | ) 14 | 15 | 16 | # Basic plots ----------------------------------- 17 | test_that("stat_kruskal_test works for basic ggplots", { 18 | bxp <- ggboxplot(df, x = "dose", y = "len") + 19 | stat_kruskal_test() 20 | bxp_build <- ggplot2::ggplot_build(bxp) 21 | stat.test <- bxp_build$data[[2]] 22 | expect_equal(as.numeric(stat.test$x), 1) 23 | expect_equal(as.numeric(stat.test$y), 36.4) 24 | expect_equal(stat.test$label, "Kruskal-Wallis, p < 0.0001") 25 | }) 26 | 27 | 28 | # Grouped plots----------------------------------- 29 | test_that("stat_kruskal_test works for grouped plots: grouped by x position", { 30 | bxp <- ggboxplot(df, x = "group", y = "len", color = "dose") + 31 | stat_kruskal_test(aes(group = dose), label = "{p.adj.format}") 32 | bxp_build <- ggplot2::ggplot_build(bxp) 33 | stat.test <- bxp_build$data[[2]] 34 | expect_equal(as.numeric(stat.test$x), c(1, 2, 3)) 35 | expect_equal(as.numeric(stat.test$y), c(36.4, 36.4, 36.4)) 36 | expect_equal(stat.test$label, c("0.0028", "0.0056", "0.0056")) 37 | }) 38 | 39 | test_that("stat_kruskal_test works for grouped plots: grouped by legend variable", { 40 | bxp <- ggboxplot(df, x = "group", y = "len", color = "dose") + 41 | stat_kruskal_test(aes(group = dose), label = "{p.format}", group.by = "legend.var") 42 | bxp_build <- ggplot2::ggplot_build(bxp) 43 | stat.test <- bxp_build$data[[2]] 44 | expect_equal(as.numeric(stat.test$x), c(0.73, 0.73, 0.73)) 45 | expect_equal(as.numeric(stat.test$y), c(36.4, 39.62, 42.84)) 46 | expect_equal(stat.test$label, c("0.012", "0.018", "0.038")) 47 | }) 48 | -------------------------------------------------------------------------------- /tests/testthat/test-stat_welch_anova_test.R: -------------------------------------------------------------------------------- 1 | context("test-stat_welch_anova_test") 2 | 3 | # Data preparation 4 | df <- ToothGrowth 5 | df$dose <- as.factor(df$dose) 6 | df$id <- rep(1:10, 6) # Add individuals id 7 | # Add a random grouping variable 8 | set.seed(123) 9 | df$group <- sample(factor(rep(c("grp1", "grp2", "grp3"), 20))) 10 | df <- df %>% mutate( 11 | len = ifelse(group == "grp2", len+2, len), 12 | len = ifelse(group == "grp3", len+7, len) 13 | ) 14 | 15 | 16 | # Basic plots ----------------------------------- 17 | test_that("stat_welch_anova_test works for basic ggplots", { 18 | bxp <- ggboxplot(df, x = "dose", y = "len") + 19 | stat_welch_anova_test() 20 | bxp_build <- ggplot2::ggplot_build(bxp) 21 | stat.test <- bxp_build$data[[2]] 22 | expect_equal(as.numeric(stat.test$x), 1) 23 | expect_equal(as.numeric(stat.test$y), 36.4) 24 | expect_equal(stat.test$label, "Welch Anova, p < 0.0001") 25 | }) 26 | 27 | 28 | # Grouped plots----------------------------------- 29 | test_that("stat_welch_anova_test works for grouped plots: grouped by x position", { 30 | bxp <- ggboxplot(df, x = "group", y = "len", color = "dose") + 31 | stat_welch_anova_test(aes(group = dose), label = "{p.adj.format}") 32 | bxp_build <- ggplot2::ggplot_build(bxp) 33 | stat.test <- bxp_build$data[[2]] 34 | expect_equal(as.numeric(stat.test$x), c(1, 2, 3)) 35 | expect_equal(as.numeric(stat.test$y), c(36.4, 36.4, 36.4)) 36 | expect_equal(stat.test$label, c("0.004", "0.004", "0.0024")) 37 | }) 38 | 39 | test_that("stat_welch_anova_test works for grouped plots: grouped by legend variable", { 40 | bxp <- ggboxplot(df, x = "group", y = "len", color = "dose") + 41 | stat_welch_anova_test(aes(group = dose), label = "{p.format}", group.by = "legend.var") 42 | bxp_build <- ggplot2::ggplot_build(bxp) 43 | stat.test <- bxp_build$data[[2]] 44 | expect_equal(as.numeric(stat.test$x), c(0.73, 0.73, 0.73)) 45 | expect_equal(as.numeric(stat.test$y), c(36.4, 39.62, 42.84)) 46 | expect_equal(stat.test$label, c("0.039", "0.023", "0.045")) 47 | }) 48 | -------------------------------------------------------------------------------- /tests/testthat/test-utils-tidyr.R: -------------------------------------------------------------------------------- 1 | 2 | # Wide data 3 | get_wide_data <- function(){ 4 | tibble::tibble( 5 | before = c(200.1, 190.9, 192.7), 6 | after = c(392.9, 393.2, 345.1) 7 | ) 8 | } 9 | 10 | 11 | test_that("df_gather is sorting rows as done by gather_()", { 12 | df <- get_wide_data() 13 | expected_output <- tibble::tribble( 14 | ~condition, ~val, 15 | "before", 200.1, 16 | "before", 190.9, 17 | 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