doc updated #300

CRAN-RELEASE

@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2020-06-27.
+Once it is accepted, delete this file and tag the release (commit 7ca7d83936).

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: ggpubr
 Type: Package
 Title: 'ggplot2' Based Publication Ready Plots
-Version: 0.3.0.999
-Date: 2020-05-03
+Version: 0.4.0
+Date: 2020-06-27
 Authors@R: c(
     person("Alboukadel", "Kassambara", role = c("aut", "cre"), email = "[email protected]"))
 Description: The 'ggplot2' package is excellent and flexible for elegant data
@@ -33,7 +33,7 @@ Imports:
     glue,
     polynom,
     rlang,
-    rstatix (>= 0.4.0),
+    rstatix (>= 0.6.0),
     tibble,
     magrittr
 Suggests:
@@ -118,4 +118,5 @@ Collate:
     'text_grob.R'
     'theme_pubr.R'
     'theme_transparent.R'
+    'utils-geom-signif.R'
     'utils-pipe.R'

NEWS.md

@@ -1,6 +1,5 @@
-# ggpubr 0.3.0.999
+# ggpubr 0.4.0
 
-To DO: merging two legends in ggarrange, discussion: https://community.rstudio.com/t/how-to-combine-two-separate-legends-side-by-side/9480/5
 
 ## New features
 

R/annotate_figure.R

@@ -3,7 +3,7 @@ NULL
 #'Annotate Arranged Figure
 #'
 #'@description Annotate figures including: i) ggplots, ii) arranged ggplots from
-#'  \code{\link{ggarrange}()}, \code{\link[gridExtra]{grid.arrange}()} and
+#'  \code{\link{ggarrange}()}, \code{\link[gridExtra:arrangeGrob]{grid.arrange}()} and
 #'  \code{\link[cowplot]{plot_grid}()}.
 #'@param p (arranged) ggplots.
 #'@param top,bottom,left,right optional string, or grob.

R/as_ggplot.R

@@ -2,11 +2,11 @@
 NULL
 #' Storing grid.arrange() arrangeGrob() and plots
 #'
-#' @description Transform the output of \code{\link[gridExtra]{arrangeGrob}()}
-#'   and \code{\link[gridExtra]{grid.arrange}()} to a an object of class ggplot.
+#' @description Transform the output of \code{\link[gridExtra:arrangeGrob]{arrangeGrob}()}
+#'   and \code{\link[gridExtra:arrangeGrob]{grid.arrange}()} to a an object of class ggplot.
 #' @param x an object of class gtable or grob as returned by the functions
-#'   \code{\link[gridExtra]{arrangeGrob}()} and
-#'   \code{\link[gridExtra]{grid.arrange}()}.
+#'   \code{\link[gridExtra:arrangeGrob]{arrangeGrob}()} and
+#'   \code{\link[gridExtra:arrangeGrob]{grid.arrange}()}.
 #' @return an object of class ggplot.
 #'
 #' @examples

R/font.R

@@ -2,7 +2,7 @@
 #'
 #'@description Change the appearance of the main title, subtitle, caption, axis
 #'  labels and text, as well as the legend title and texts. Wrapper around
-#'  \code{\link[ggplot2]{element_text}()}.
+#'  \code{\link[ggplot2:element]{element_text}()}.
 #'
 #'@param object character string specifying the plot components. Allowed values
 #'  include: \itemize{ \item \code{"title"} for the main title \item
@@ -23,7 +23,7 @@
 #'  "bold.italic"}).
 #'@param family the font family.
 #'@param ... other arguments to pass to the function
-#'  \code{\link[ggplot2]{element_text}()}.
+#'  \code{\link[ggplot2:element]{element_text}()}.
 #'
 #'@examples
 #'# Load data

R/get_breaks.R

@@ -1,8 +1,8 @@
 #' Easy Break Creation for Numeric Axes
 #'
 #' @description Creates breaks for numeric axes to be used in the functions
-#'   \code{\link[ggplot2]{scale_x_continuous}()} and
-#'   \code{\link[ggplot2]{scale_y_continuous}()}. Can be used to increase the
+#'   \code{\link[ggplot2:scale_continuous]{scale_x_continuous}()} and
+#'   \code{\link[ggplot2:scale_continuous]{scale_y_continuous}()}. Can be used to increase the
 #'   number of x and y ticks by specifying the option \code{n}. It's also
 #'   possible to control axis breaks by specifying a step between ticks.  For
 #'   example, if \code{by = 5}, a tick mark is shown on every 5.

R/get_palette.R

@@ -4,7 +4,7 @@
 #'  palettes and custom color palettes. Useful to extend RColorBrewer and ggsci to support more colors.
 #'@param palette Color palette. Allowed values include: \itemize{ \item
 #'  \strong{Grey color palettes}: "grey" or "gray"; \item \strong{RColorBrewer
-#'  palettes}, see \code{\link[RColorBrewer]{brewer.pal}} and details section.
+#'  palettes}, see \code{\link[RColorBrewer:ColorBrewer]{brewer.pal}} and details section.
 #'  Examples of palette names include: "RdBu", "Blues", "Dark2", "Set2", ...;
 #'  \item \strong{Custom color palettes}. For example, palette = c("#00AFBB",
 #'  "#E7B800", "#FC4E07"); \item \strong{ggsci scientific journal palettes},

R/ggscatter.R

@@ -29,7 +29,7 @@ NULL
 #'
 #'  \itemize{ \item \code{"convex"}: plot convex hull of a set o points. \item
 #'  \code{"confidence"}: plot confidence ellipses arround group mean points as
-#'  \code{\link[FactoMineR]{coord.ellipse}()}[in FactoMineR]. \item \code{"t"}:
+#'  \code{FactoMineR::coord.ellipse()}. \item \code{"t"}:
 #'  assumes a multivariate t-distribution. \item \code{"norm"}: assumes a
 #'  multivariate normal distribution. \item \code{"euclid"}: draws a circle with
 #'  the radius equal to level, representing the euclidean distance from the

R/ggscatterhist.R

@@ -12,7 +12,7 @@ NULL
 #'@param margin.plot the type of the marginal plot. Default is "hist".
 #'@param margin.params parameters to be applied to the marginal plots.
 #'@param margin.ggtheme the theme of the marginal plot. Default is
-#'  \code{\link[ggplot2]{theme_void}()}.
+#'  \code{\link[ggplot2:ggtheme]{theme_void}()}.
 #'@param margin.space logical value. If TRUE, adds space between the main plot
 #'  and the marginal plot.
 #'@param bins Number of histogram bins. Defaults to 30. Pick a better value that

R/ggsummarystats.R

@@ -4,7 +4,7 @@ NULL
 #' GGPLOT with Summary Stats Table Under the Plot
 #'
 #' @description Create a ggplot with summary stats (n, median, mean, iqr) table
-#'   under the plot.
+#'   under the plot. Read more: \href{https://www.datanovia.com/en/blog/how-to-create-a-beautiful-plots-in-r-with-summary-statistics-labels/}{How to Create a Beautiful Plots in R with Summary Statistics Labels}.
 #' @inheritParams ggboxplot
 #' @param digits integer indicating the number of decimal places (round) to be
 #'   used.
@@ -79,14 +79,7 @@ NULL
 #'
 #' # Facet
 #' #::::::::::::::::::::::::::::::::::::::::::::::::
-#'
-#' ggsummarystats(
-#'   df, x = "dose", y = "len",
-#'   ggfunc = ggboxplot, add = "jitter",
-#'   color = "dose", palette = "npg",
-#'   facet.by = c("supp", "qc")
-#' )
-#'  # Specify labeller
+#' # Specify free.panels = TRUE for free panels
 #' ggsummarystats(
 #'   df, x = "dose", y = "len",
 #'   ggfunc = ggboxplot, add = "jitter",
@@ -95,15 +88,6 @@ NULL
 #'   labeller = "label_both"
 #' )
 #'
-#' # Free panels
-#' ggsummarystats(
-#'   df, x = "dose", y = "len",
-#'   ggfunc = ggboxplot, add = "jitter",
-#'   color = "dose", palette = "npg",
-#'   facet.by = c("supp", "qc"),
-#'   free.panels = TRUE, labeller = "label_both"
-#' )
-#'
 #' @describeIn ggsummarystats Create a table of summary stats
 #' @export
 ggsummarytable <- function(data, x, y, digits = 0, size = 3, color = "black", palette = NULL,

R/reexports.R

@@ -4,9 +4,6 @@ dplyr::mutate
 #' @importFrom dplyr group_by
 #' @export
 dplyr::group_by
-#' @importFrom ggsignif geom_signif
-#' @export
-ggsignif::geom_signif
 #' @importFrom rstatix get_summary_stats
 #' @export
 rstatix::get_summary_stats

R/rotate_axis_text.R

@@ -10,7 +10,7 @@
 #'@param hjust horizontal justification (in [0, 1]).
 #'@param vjust vertical justification (in [0, 1]).
 #'@param ... other arguments to pass to the function
-#'  \code{\link[ggplot2]{element_text}()}.
+#'  \code{\link[ggplot2:element]{element_text}()}.
 #'
 #'@examples
 #'# Load data

R/stat_central_tendency.R

@@ -13,7 +13,7 @@ NULL
 #'   For continuous variable, we can consider using mean or median as the
 #'   measures of the central tendency.
 #' @inheritParams ggplot2::layer
-#' @param ... other arguments to pass to \code{\link[ggplot2]{geom_line}}.
+#' @param ... other arguments to pass to \code{\link[ggplot2:geom_path]{geom_line}}.
 #' @param na.rm If FALSE (the default), removes missing values with a warning.
 #'   If TRUE silently removes missing values.
 #' @param type the type of central tendency measure to be used. Possible values

R/stat_compare_means.R

@@ -41,7 +41,7 @@ NULL
 #'@param step.increase numeric vector with the increase in fraction of total
 #'  height for every additional comparison to minimize overlap.
 #'@param ... other arguments to pass to \code{\link[ggplot2]{geom_text}} or
-#'  \code{\link[ggplot2]{geom_label}}.
+#'  \code{\link[ggplot2:geom_text]{geom_label}}.
 #'@param na.rm If FALSE (the default), removes missing values with a warning. If
 #'  TRUE silently removes missing values.
 #'@seealso \code{\link{compare_means}}

R/stat_conf_ellipse.R

@@ -2,7 +2,7 @@
 NULL
 #' Plot confidence ellipses.
 #' @description Plot confidence ellipses around barycenters. The method for
-#'   computing confidence ellipses has been modified from FactoMineR::coord.ellipse.
+#'   computing confidence ellipses has been modified from \code{FactoMineR::coord.ellipse()}.
 #' @inheritParams ggplot2::layer
 #' @inheritParams ggplot2::stat_ellipse
 #' @param level confidence level used to construct the ellipses. By

R/stat_cor.R

@@ -39,7 +39,7 @@ NULL
 #'  precision for the p-value. Default is NULL. Use (e.g.) 0.0001 to show 4
 #'  decimal places of precision. If specified, then \code{p.digits} is ignored.
 #'@param ... other arguments to pass to \code{\link[ggplot2]{geom_text}} or
-#'  \code{\link[ggplot2]{geom_label}}.
+#'  \code{\link[ggplot2:geom_text]{geom_label}}.
 #'@param na.rm If FALSE (the default), removes missing values with a warning. If
 #'  TRUE silently removes missing values.
 #'@seealso \code{\link{ggscatter}}

R/stat_overlay_normal_density.R

@@ -6,7 +6,7 @@ NULL
 #'   density distribution of 'x'. This is useful for visually inspecting the
 #'   degree of deviance from normality.
 #' @inheritParams ggplot2::layer
-#' @param ... other arguments to pass to \code{\link[ggplot2]{geom_line}}.
+#' @param ... other arguments to pass to \code{\link[ggplot2:geom_path]{geom_line}}.
 #' @param na.rm If FALSE (the default), removes missing values with a warning.
 #'   If TRUE silently removes missing values.
 #' @seealso \code{\link{ggdensity}}

R/stat_regline_equation.R

@@ -21,7 +21,7 @@ NULL
 #'  for absolute positioning of the label. If too short they will be recycled.
 #'@param output.type character One of "expression", "latex" or "text".
 #'@param ... other arguments to pass to \code{\link[ggplot2]{geom_text}} or
-#'  \code{\link[ggplot2]{geom_label}}.
+#'  \code{\link[ggplot2:geom_text]{geom_label}}.
 #'@param na.rm If FALSE (the default), removes missing values with a warning. If
 #'  TRUE silently removes missing values.
 #'@seealso \code{\link{ggscatter}}

R/text_grob.R

@@ -3,15 +3,15 @@ NULL
 
 #' Create a Text Graphical object
 #' @description Create easily a customized text grob (graphical object). Wrapper around
-#'   \code{\link[grid]{textGrob}}.
+#'   \code{\link[grid:grid.text]{textGrob}}.
 #' @inheritParams grid::grid.text
 #' @param color text font color.
 #' @param face font face. Allowed values include one of \code{"plain", "bold",
 #'   "italic", "bold.italic"}.
 #' @param size font size (e.g.: size = 12)
 #' @param lineheight line height (e.g.: lineheight = 2).
 #' @param family font family.
-#' @param ... other arguments passed to \link[grid]{textGrob}.
+#' @param ... other arguments passed to \link[grid:grid.text]{textGrob}.
 #' @return  a text grob.
 #' @examples
 #'text <- paste("iris data set gives the measurements in cm",

R/utils-geom-signif.R

@@ -0,0 +1,10 @@
+#' geom_signif exported from ggsignif package
+#'
+#' See \code{ggsignif::\link[ggsignif:stat_signif]{geom_signif}} for details.
+#'
+#' @name geom_signif
+#' @rdname geom_signif
+#' @keywords internal
+#' @export
+#' @importFrom ggsignif geom_signif
+NULL

_pkgdown.yml

@@ -86,15 +86,17 @@ reference:
       - ggexport
       - annotate_figure
       - background_image
+  - title: Make Programming Easy with GGPlot2
+    contents:
+      - geom_exec
+      - create_aes
   - title: Helpers
     contents:
       - facet
       - add_summary
       - ggadd
       - get_palette
       - as_ggplot
-      - geom_exec
-      - create_aes
   - title: Data
     contents:
       - diff_express

cran-comments.md

@@ -1,5 +1,5 @@
 ## Test environments
-* local OS X install, R 3.3.2
+* local OS X install, R 3.6.0
 * win-builder 
 * Travis
 
@@ -13,5 +13,5 @@ All packages that I could install passed.
 
 ## Update
 
-This is an update version 0.3.0 (see NEWS.md).
+This is an update version 0.4.0 (see NEWS.md).