diff --git a/README.md b/README.md
index 6f6c6f4f2eead422c4644ef41b47cb6b798e9649..3adb0b3282fc4facf4dc070d18209be931a9e6ca 100644
--- a/README.md
+++ b/README.md
@@ -1,174 +1,258 @@
-#### DESCRIPTION
+[//]: # "#to make links in gitlab: example with racon https://github.com/isovic/racon"
+[//]: # "tricks in markdown: https://openclassrooms.com/fr/courses/1304236-redigez-en-markdown"
+
+| usage | R dependencies |
+| --- | --- |
+| [](https://cran.r-project.org/mirrors.html) | [](https://cran.r-project.org/mirrors.html) |
+| [-green?style=plastic)](https://www.gnu.org/licenses) | [](http://www.rforge.net/car/) |
+| | [](http://www.rforge.net/carData/) |
+| | [](http://www.rforge.net/emmeans/) |
+| | [](https://github.com/tidyverse/ggplot2) |
+| | [](http://www.rforge.net/lemon/) |
+| | [](http://www.rforge.net/lme4/) |
+| | [](http://www.rforge.net/lmerTest/) |
+| | [](https://github.com/tidyverse/lubridate) |
+| | [](http://www.rforge.net/Matrix/) |
+| | [](https://gitlab.pasteur.fr/gmillot/cute_little_R_functions) |
+
+
+## TABLE OF CONTENTS
+
+ - [AIM](#aim)
+ - [REPOSITORY CONTENT](#repository-content)
+ - [DESCRIPTIONS OF THE FUNCTIONS](#description-of-the-functions)
+ - [HOW TO HOW TO LOAD AND MANIPULATE](#how-to-load-and-manipulate)
+ - [VERSIONS](#versions)
+ - [LICENCE](#licence)
+ - [CITATION](#citation)
+ - [CREDITS](#credits)
+ - [ACKNOWLEDGEMENTS](#Acknowledgements)
+ - [WHAT'S NEW IN](#what's-new-in)
-Cute Little R Functions contains 42 functions for R/RStudio that facilitate basic procedures in 1) object analysis, 2) object modification, 3) graphic handling and 4) log file management.
-The function names are:
+## AIM
-## Object analysis
-fun_param_check() #### check class, type, length, etc., of objects
-fun_object_info() #### recover object information
-fun_1D_comp() #### comparison of two 1D datasets (vectors, factors, 1D tables)
-fun_2D_comp() #### comparison of two 2D datasets (row & col names, dimensions, etc.)
-fun_2D_head() #### head of the left or right of big 2D objects
-fun_2D_tail() #### tail of the left or right of big 2D objects
-fun_list_comp() #### comparison of two lists
+Set of functions that facilitate basic procedures in 1) object analysis, 2) object modification, 3) graphic handling and 4) log file management.
+The present repository of Cute Little R functions is for beta testing. Ultimately, functions will be provided as packages
-## Object modification
-fun_name_change() #### check a vector of character strings and modify any string if present in another vector
-fun_dataframe_remodeling() #### remodeling a data frame to have column name as a qualitative values and vice-versa
-fun_refactorization() #### remove classes that are not anymore present in factors or factor columns in data frames
-fun_round() #### rounding number if decimal present
-fun_90clock_matrix_rot() #### 90° clockwise matrix rotation
-fun_num2color_mat() #### convert a numeric matrix into hexadecimal color matrix
-fun_by_case_matrix_op() #### assemble several matrices with operation
-fun_mat_inv() #### return the inverse of a square matrix
-fun_mat_fill() #### fill the empty half part of a symmetric square matrix
-fun_perm() #### progressively breaks a vector order
-fun_perm_consec() #### progressively breaks a vector order
+## REPOSITORY CONTENT
-## Graphics management
+**cute_little_R_functions.R** file that has to be sourced in R or RStudio
-fun_window_width_resizing() #### window width depending on classes to plot
-fun_open_window() #### open a GUI or pdf graphic window
-fun_prior_plot() #### set graph param before plotting
-fun_scale() #### select nice numbers when setting breaks on an axis
-fun_post_plot() #### set graph param after plotting
-fun_close_specif_window() #### close specific graphic windows
+**cute_little_R_functions.docx** same as cute_little_R_functions.R but for better reading (interactive outline at the beginning of the file)
+**examples.R** examples of all the functions, except fun_gg_boxplot() and fun_gg_scatter(), that can be sourced or copied-pasted
-## Standard graphics
+**boxplot_examples.R** examples of fun_gg_boxplot() that can be sourced or copied-pasted
-fun_empty_graph() #### text to display for empty graphs
+**scatter_examples.R** examples of fun_gg_scatter() that can be sourced or copied-pasted
+**other** folder containing avorted developments
-## gg graphics
-fun_gg_palette() #### ggplot2 default color palette
-fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle
-fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally)
-fun_gg_bar_mean() #### ggplot2 mean barplot + overlaid dots if required
-fun_gg_boxplot() #### ggplot2 boxplot + background dots if required
-fun_gg_bar_prop() #### ggplot2 proportion barplot
-fun_gg_strip() #### ggplot2 stripchart + mean/median
-fun_gg_violin() #### ggplot2 violins
-fun_gg_line() #### ggplot2 lines + background dots and error bars
-fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required
-fun_gg_empty_graph() #### text to display for empty graphs
+## DESCRIPTIONS OF THE FUNCTIONS
+| Object analysis | |
+| --- | --- |
+| **fun_check() | check class, type, length, etc., of objects |
+| **fun_secu() | verif that local variables are not present in other envs |
+| **fun_info() | recover object information |
+| **fun_head() | head of the left or right of big 2D objects |
+| **fun_tail() | tail of the left or right of big 2D objects |
+| **fun_comp_1d() | comparison of two 1D datasets (vectors, factors, 1D tables) |
+| **fun_comp_2d() | comparison of two 2D datasets (row & col names, dimensions, etc.) |
+| **fun_comp_list() | comparison of two lists |
+| **fun_test() | test combinations of argument values of a function and return errors (and graphs) |
-## Graphic extraction
+| Object modification | |
+| --- | --- |
+| **fun_name_change() | check a vector of character strings and modify any string if present in another vector |
+| **fun_df_remod() | remodeling a data frame to have column name as a qualitative values and vice-versa |
+| **fun_round() | rounding number if decimal present |
+| **fun_mat_rotate() | 90° clockwise matrix rotation |
+| **fun_mat_num2color() | convert a numeric matrix into hexadecimal color matrix |
+| **fun_mat_op() | assemble several matrices with operation |
+| **fun_mat_inv() | return the inverse of a square matrix |
+| **fun_mat_fill() | fill the empty half part of a symmetric square matrix |
+| **fun_permut() | progressively breaks a vector order |
+| **fun_slide() | return a computation made on a vector using a sliding window |
-fun_var_trim_display() #### display values from a quantitative variable and trim according to defined cut-offs
-fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation
+| Graphics management | |
+| --- | --- |
+| **fun_width() | window width depending on classes to plot |
+| **fun_open() | open a GUI or pdf graphic window |
+| **fun_prior_plot() | set graph param before plotting (erase axes for instance) |
+| **fun_scale() | select nice label numbers when setting number of ticks on an axis |
+| **fun_inter_ticks() | define coordinates of secondary ticks |
+| **fun_post_plot() | set graph param after plotting (axes redesign for instance) |
+| **fun_close() | close specific graphic windows |
+| Standard graphics | |
+| --- | --- |
+| **fun_empty_graph() | text to display for empty graphs |
-## Import
+| gg graphics | |
+| --- | --- |
+| **fun_gg_palette() | ggplot2 default color palette |
+| **fun_gg_just() | ggplot2 justification of the axis labeling, depending on angle |
+| **fun_gg_get_legend() | get the legend of ggplot objects |
+| **fun_gg_point_rast() | ggplot2 raster scatterplot layer |
+| **fun_gg_boxplot() | ggplot2 boxplot + background dots if required |
+| **fun_gg_scatter() | ggplot2 scatterplot + lines (up to 6 overlays totally) |
+| **fun_gg_empty_graph() | text to display for empty graphs |
-fun_pack_import() #### check if R packages are present and import into the working environment
-fun_python_pack_import() #### check if python packages are present
+| Graphic extraction | |
+| --- | --- |
+| **fun_trim() | display values from a quantitative variable and trim according to defined cut-offs |
+| **fun_segmentation() | segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation |
+| Import | |
+| --- | --- |
+| **fun_pack() | check if R packages are present and import into the working environment |
+| **fun_python_pack() | check if python packages are present |
-## Exporting results (text & tables)
+| Print / Exporting results (text & tables) | |
+| --- | --- |
+| **fun_report() | print string or data object into output file |
+| **fun_get_message() | return error/warning/other messages of an expression (that can be exported) |
-fun_export_data() #### print string or data object into output file
+## HOW TO LOAD AND MANIPULATE cute_little_R_functions
+Download the desired Tagged version, never the current master, at https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/tags
-#### LICENCE
+ For that:
-This package of scripts can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-Distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-See the GNU General Public License for more details at https://www.gnu.org/licenses.
-
-
-
-
-#### CREDITS
-
-Gael A. Millot, Hub-C3BI, Institut Pasteur, USR 3756 IP CNRS, Paris, France
-
-
-
-
-#### HOW TO USE IT
-
-1) Download the desired Tagged version, never the current master, at https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/tags
+ 1) Select the desired tagged release
+
+ 2) Browse files
+
+ 3) Display the cute_little_R_functions.R as raw file
+
+ 4) Source the file using the url address. Example
+ `
+ source("https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/557976d693e37b499b89c76e4b2142846eb89d5b/cute_little_R_functions.R")
+ `
-2) Directly source the cute_little_R_functions.R into R/RStudio to have the functions available in the working environment, using for instance source("https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v6.0.0/cute_little_R_functions.R")
Description of the functions is at the beginning of the function body. To obtain it:
Either read the cute_little_functions.docx (or open the cute_little_R_functions.R file).
- Or in the R/RStudio console, type the name of the function without brackets. Example : fun_object_info.
+ Or in the R/RStudio console, type the name of the function without brackets. Example : `fun_info`.
+## VERSIONS
+The different releases are tagged [here](https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/tags)
-#### FILE DESCRIPTIONS
-cute_little_R_functions.R file that has to be sourced
-cute_little_R_functions.docx file that facilitate reading of the function description
-examples_alone.txt compile all the examples of the functions into a single file
+## LICENCE
+This package of scripts can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+Distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchandability or fitness for a particular purpose.
+See the GNU General Public License for more details at https://www.gnu.org/licenses.
+## CITATION
-#### WEB LOCATION
+Not yet published
-Check for updated versions (most recent tags) at https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/tags
+## CREDITS
+[Gael A. Millot](https://gitlab.pasteur.fr/gmillot), Hub-CBD, Institut Pasteur, USR 3756 IP CNRS, Paris, France
-#### WHAT'S NEW IN
+## ACKNOWLEDGEMENTS
+R and R packages developers
-## v6.0.0
+Gitlab developers
+
+
+## WHAT'S NEW IN
+
+### v6.0.0
1) name of functions changed:
+
fun_param_check() fun_check()
+
fun_object_info() fun_info()
+
fun_1D_comp() fun_comp_1d()
+
fun_2D_comp() fun_comp_2d()
+
fun_list_comp() fun_comp_list()
+
fun_2D_head() fun_head()
+
fun_2D_tail() fun_tail()
+
fun_dataframe_remodeling() fun_df_remod()
+
fun_by_case_matrix_op() fun_mat_op()
+
fun_rounding() fun_round()
+
fun_90clock_matrix_rot() fun_mat_rotate()
+
fun_hexa_hsv_color_matrix() fun_mat_num2color()
+
fun_graph_param_prior_plot() fun_prior_plot()
+
fun_feature_post_plot() fun_post_plot()
+
fun_window_width_resizing() fun_width()
+
fun_open_window() fun_open()
+
fun_close_specif_window() fun_close()
+
fun_var_trim_display() fun_trim()
+
fun_export_data() fun_report()
+
+
2) new functions added:
+
fun_name_change()
+
fun_mat_fill()
+
fun_permut()
+
fun_permut_consec()
+
fun_empty_graph()
+
fun_gg_palette()
+
fun_gg_just()
+
fun_gg_point_rast()
+
fun_gg_scatter()
-fun_gg_bar()
-fun_gg_heatmap()
+
fun_gg_empty_graph()
+
fun_segmentation()
+
fun_pack()
+
fun_python_pack()
+
fun_warning()
+
+
3) text error modified in fun_head() and fun_tail(), + deals without all objects but use head() and tail() if not 2D object
4) in fun_param_check(): (1) has now the class = "vector", (2) argument fun.name added
@@ -178,69 +262,72 @@ fun_warning()
6) Functions checked for R version 3.6.1
7) function deprecated:
+
fun_refactorization()
-## v5.1.0
+### v5.1.0
1) bugs corrected in fun_2D_head() and fun_2D_tail() functions
-## v5.0.0
+### v5.0.0
1) fun_2D_head() function added
+
2) fun_2D_tail() function added
+
3) argument "noquote" added in fun_export_data()
-## v4.9.0
+### v4.9.0
1) fun_mat_inv() function added
-## v4.8.0
+### v4.8.0
1) magnific argument removed in fun_feature_post_plot() because no need anymore
-## v4.7.0
+### v4.7.0
1) check of numeric arguments: class = "numeric" -> mode = "numeric" to allow for integers values in these arguments
-## v4.6.0
+### v4.6.0
1) fun_by_case_matrix_op() added
-## v4.5.0
+### v4.5.0
1) fun_open_window() improved to deal with Linux systems
2) fun_graph_param_prior_plot() improved to deal with Linux systems
-## v4.4.0
+### v4.4.0
1) fun_dataframe_remodeling() now add a ini_rowname column in the output data frame when it is coherent and when initial row names are available (not NULL)
-## v4.3.0
+### v4.3.0
1) fun_object_info() now manages object class "ordered" "factor"
-## v4.2.0
+### v4.2.0
1) bug in the fun_2D_comp() function fixed
-## v4.1.0
+### v4.1.0
1) text.corner replaced by corner.text everywhere
-## v4.0.0
+### v4.0.0
1) fun_var_trim_display() function added
@@ -251,14 +338,14 @@ fun_refactorization()
4) error messages now mention the function that generates this message
-## v3.1.0
+### v3.1.0
1) fun_export_data() function modified: argument data cannot be NULL
2) the debugging line containing r_debugging_tools-v1.2.R updated for the new position of this script
-## v3.0.0
+### v3.0.0
1) cute_little_functions.R renamed cute_little_R_functions.R
@@ -267,12 +354,12 @@ fun_refactorization()
3) more examples added, also draws added in the .docx file for fun_dataframe_remodeling()
-## v2.0.1
+### v2.0.1
1) functions that use other functions from this toolset now check if these required functions are indeed present in the R environment
-## v2.0.0
+### v2.0.0
1) fun_feature_post_plot() function improved: Now independent magnification for x axis/labels and y axis/labels. BEWARE: argument names have been modified
@@ -281,7 +368,13 @@ fun_refactorization()
3) Bug corrected in fun_refactorization() function
-## v1.3
+### v1.3
+
+Everything
+
+
+
+
1) fun_1D_comp() function improved: provide the common elements, common names and common levels if exist
diff --git a/cute_little_R_functions.R b/cute_little_R_functions.R
index ebdb421e8ffef3161d3134e6017e3ef0d3842a55..fa0bcd327195991bf21966b51d6ecd97de590d9e 100644
--- a/cute_little_R_functions.R
+++ b/cute_little_R_functions.R
@@ -7966,7 +7966,6 @@ return(output) # do not use cat() because the idea is to reuse the message
-# remain to solve the justification of the text
# check s/lapply everywhere with get: done cute boxplot scatter
# get() with env everywhere: done cute boxplot scatter
# add the new NA and NULL check cute, boxplot, scatter: done boxplot, scatter
@@ -8011,7 +8010,7 @@ y.bottom.extra.margin = 0.05,
stat.disp = "top",
stat.disp.mean = FALSE,
stat.size = 4,
-stat.dist = 2,
+stat.dist = 5,
stat.angle = 0,
vertical = TRUE,
text.size = 12,
@@ -8091,7 +8090,7 @@ lib.path = NULL
# stat.disp: add the median number above the corresponding box. Either NULL (no number shown), "top" (at the top of the plot region) or "above" (above each box)
# stat.disp.mean: logical. Display mean numbers instead of median numbers? Ignored if stat.disp is NULL
# stat.size: numeric value of the stat font size in mm. Ignored if stat.disp is NULL
-# stat.dist: numeric value of the stat distance (in the unit of the hjust and vjust arguments of ggplot2::annotate() function). Increase the value to increase the distance from the box plot. Ignored if stat.disp is NULL or "top"
+# stat.dist: numeric value of the stat distance in percentage of the y-axis range (stat.dist = 5 means move the number displayed at 5% of the y-axis range). Ignored if stat.disp is NULL or "top"
# stat.angle: integer value of the angle of stat, using the same rules as in ggplot2. Positive values for counterclockwise rotation: 0 for horizontal, 90 for vertical, 180 for upside down etc. Negative values for clockwise rotation: 0 for horizontal, -90 for vertical, -180 for upside down etc.
# vertical: logical. Vertical boxes? WARNING: will be automatically set to TRUE if y.log argument is other than "no". Indeed, not possible to have horizontal boxes with a log axis, due to a bug in ggplot2 (see https://github.com/tidyverse/ggplot2/issues/881)
# text.size: numeric value of the font size of the (1) axis numbers, (2) axis labels and (3) texts in the graphic legend (in mm)
@@ -8142,8 +8141,7 @@ lib.path = NULL
# $sup.whisker.edge: coordinates of top whisker edges (x and xend)
# $inf.whisker.edge: coordinates of bottom whisker edges(x and xend)
# $mean: diamond mean coordinates (only if box.mean argument is TRUE)
-# $stat.display.positive: coordinates of stat numbers when positive (only if stat.disp argument is TRUE)
-# $stat.display.negative: coordinates of stat numbers when negative (only if stat.disp argument is TRUE)
+# $stat.display: coordinates of stat numbers (only if stat.disp argument is not NULL)
# y.second.tick.positions: coordinates of secondary ticks (only if y.second.tick.nb argument is non-NULL or if y.log argument is different from "no")
# y.second.tick.values: values of secondary ticks. NULL except if y.second.tick.nb argument is non-NULL or if y.log argument is different from "no")
# $panel: the variable names used for the panels (NULL if no panels). WARNING: NA can be present according to ggplot2 upgrade to v3.3.0
@@ -8155,7 +8153,7 @@ lib.path = NULL
# DEBUGGING
# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Categ1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; set.seed(NULL) ; obs1$Time[1:10] <- NA ; data1 = obs1 ; y = "Time" ; categ = c("Categ1") ; categ.class.order = NULL ; box.legend.name = NULL ; categ.color = c("green") ; box.fill = FALSE ; box.width = 0.5 ; box.space = 0.1 ; box.notch = FALSE ; box.line.size = 0.5 ; box.alpha = 0.5 ; box.mean = TRUE ; box.whisker.kind = "std" ; box.whisker.width = 0.5 ; dot.color = "black" ; dot.categ = "Categ1"; dot.categ.class.order = c("G", "H") ; dot.legend.name = NULL ; dot.tidy = TRUE ; dot.tidy.bin.nb = 50 ; dot.jitter = 0.25 ; dot.size = 3 ; dot.alpha = 0.5 ; dot.border.size = 0.5 ; dot.border.color = NULL ; y.lim = NULL ; y.log = "no" ; y.tick.nb = NULL ; y.second.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; stat.disp = NULL ; stat.disp.mean = FALSE ; stat.size = 4 ; stat.dist = 2 ; stat.angle = 0 ; x.lab = NULL ; y.lab = NULL ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; legend.show = TRUE ; legend.width = 0.5 ; x.angle = 0 ; article = FALSE ; grid = FALSE ; return = TRUE ; return.ggplot = FALSE ; return.gtable = FALSE ; plot = TRUE ; add = NULL ; warn.print = FALSE ; lib.path = NULL
# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Categ1 = rep(c("G", "H"), each = 10), Categ2 = rep(c("A", "B"), time = 10), Categ3 = rep(c("I", "J"), time = 10), stringsAsFactors = TRUE) ; set.seed(NULL) ; obs1$Time[1:10] <- NA ; data1 = obs1 ; y = "Time" ; categ = c("Categ1", "Categ2") ; categ.class.order = list(c("G", "H"), c("A", "B")); box.legend.name = NULL ; categ.color = c("green", "blue") ; box.fill = FALSE ; box.width = 0.5 ; box.space = 0.1 ; box.notch = FALSE ; box.line.size = 0.5 ; box.alpha = 0.5 ; box.mean = TRUE ; box.whisker.kind = "std" ; box.whisker.width = 0.5 ; dot.color = "black" ; dot.categ = "Categ1" ; dot.categ.class.order = NULL ; dot.legend.name = NULL ; dot.tidy = TRUE ; dot.tidy.bin.nb = 30 ; dot.jitter = 0.25 ; dot.size = 3 ; dot.alpha = 0.5 ; dot.border.size = 0.5 ; dot.border.color = NULL ; y.lim = NULL ; y.log = "no" ; y.tick.nb = NULL ; y.second.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; stat.disp = NULL ; stat.disp.mean = FALSE ; stat.size = 4 ; stat.dist = 2 ; stat.angle = 0 ; x.lab = NULL ; y.lab = NULL ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; legend.show = TRUE ; legend.width = 0.5 ; x.angle = 0 ; article = FALSE ; grid = FALSE ; return = FALSE ; return.ggplot = FALSE ; return.gtable = FALSE ; plot = TRUE ; add = NULL ; warn.print = FALSE ; lib.path = NULL
-# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Categ1 = rep(c("G", "H"), each = 10), Categ2 = rep(c("A", "B"), time = 10), stringsAsFactors = TRUE) ; set.seed(NULL) ; data1 = obs1 ; y = "Time" ; categ = c("Categ1") ; categ.class.order = list(c("H", "G")); box.legend.name = NULL ; categ.color = c("blue") ; box.fill = FALSE ; box.width = 0.5 ; box.space = 0.1 ; box.notch = TRUE ; box.line.size = 1 ; box.alpha = 1 ; box.mean = FALSE ; box.whisker.kind = "max" ; box.whisker.width = 0 ; dot.color = "black" ; dot.categ = "Categ1" ; dot.categ.class.order = NULL ; dot.legend.name = NULL ; dot.tidy = TRUE ; dot.tidy.bin.nb = 30 ; dot.jitter = 0.25 ; dot.size = 3 ; dot.alpha = 0.5 ; dot.border.size = 0.5 ; dot.border.color = NULL ; y.lim = NULL ; y.log = "log10" ; y.tick.nb = NULL ; y.second.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; stat.disp = NULL ; stat.disp.mean = FALSE ; stat.size = 4 ; stat.dist = 2 ; stat.angle = 0 ; x.lab = NULL ; y.lab = NULL ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; legend.width = 0.5 ; legend.show = TRUE ; x.angle = 0 ; article = FALSE ; grid = FALSE ; return = FALSE ; return.ggplot = FALSE ; return.gtable = FALSE ; plot = TRUE ; add = NULL ; warn.print = FALSE ; lib.path = NULL
+# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Categ1 = rep(c("G", "H"), each = 10), Categ2 = rep(c("A", "B"), time = 10), stringsAsFactors = TRUE) ; set.seed(NULL) ; data1 = obs1 ; y = "Time" ; categ = c("Categ1") ; categ.class.order = list(c("H", "G")); box.legend.name = NULL ; categ.color = c("blue") ; box.fill = FALSE ; box.width = 0.5 ; box.space = 0.1 ; box.notch = TRUE ; box.line.size = 1 ; box.alpha = 1 ; box.mean = FALSE ; box.whisker.kind = "max" ; box.whisker.width = 0 ; dot.color = "black" ; dot.categ = "Categ1" ; dot.categ.class.order = NULL ; dot.legend.name = NULL ; dot.tidy = TRUE ; dot.tidy.bin.nb = 30 ; dot.jitter = 0.25 ; dot.size = 3 ; dot.alpha = 0.5 ; dot.border.size = 0.5 ; dot.border.color = NULL ; y.lim = NULL ; y.log = "log10" ; y.tick.nb = NULL ; y.second.tick.nb = NULL ; y.include.zero = FALSE ; y.top.extra.margin = 0.05 ; y.bottom.extra.margin = 0.05 ; stat.disp = "above" ; stat.disp.mean = FALSE ; stat.size = 4 ; stat.dist = 2 ; stat.angle = 0 ; x.lab = NULL ; y.lab = NULL ; vertical = TRUE ; text.size = 12 ; title = "" ; title.text.size = 8 ; legend.width = 0.5 ; legend.show = TRUE ; x.angle = 0 ; article = FALSE ; grid = FALSE ; return = FALSE ; return.ggplot = FALSE ; return.gtable = FALSE ; plot = TRUE ; add = NULL ; warn.print = FALSE ; lib.path = NULL
# function name
function.name <- paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
arg.user.setting <- as.list(match.call(expand.dots = FALSE))[-1] # list of the argument settings (excluding default values not provided by the user)
@@ -9055,12 +9053,22 @@ assign(paste0(tempo.gg.name, tempo.gg.count <- tempo.gg.count + 1), ggplot2::sca
tempo.cat <- paste0("INTERNAL CODE ERROR IN ", function.name, "\nCODE INCONSISTENCY 1")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", ifelse(is.null(warn), "", paste0("IN ADDITION\nWARNING", ifelse(warn.count > 1, "S", ""), ":\n\n", warn))), call. = FALSE) # == in stop() to be able to add several messages between ==
}
-stat.just <- fun_gg_just(angle = stat.angle, pos = ifelse(vertical == TRUE, "top", "right"), kind = "text")
+if( ! is.null(stat.disp)){
+stat.just <- fun_gg_just(
+angle = stat.angle,
+pos = ifelse(
+vertical == TRUE,
+ifelse(stat.disp == "top", "bottom", "top"), # "bottom" because we want justification for text that are below the ref point which is the top of the graph. The opposite for "above"
+ifelse(stat.disp == "top", "left", "right") # "left" because we want justification for text that are on the left of the ref point which is the right border of the graph. The opposite for "above"
+),
+kind = "text"
+)
+}
# has in fact no interest because ggplot2 does not create room for geom_text()
tempo.data.max <- data1[which.max(data1[, y]), ]
tempo.data.max <- data.frame(tempo.data.max, label = formatC(tempo.data.max[, y], digit = 2, drop0trailing = TRUE, format = "f"))
# end has in fact no interest because ggplot2 does not create room for geom_text()
-tempo.graph.info.ini <- ggplot2::ggplot_build(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if( ! is.null(stat.disp)){' + ggplot2::geom_text(data = tempo.data.max, mapping = ggplot2::aes_string(x = 1, y = y, label = "label"), size = stat.size, color = "black", angle = stat.angle, hjust = ifelse(vertical == TRUE, stat.just$hjust, stat.just$hjust - stat.dist), vjust = ifelse(vertical == TRUE, stat.just$vjust - stat.dist, stat.just$vjust))'})))) # added here to have room for annotation
+tempo.graph.info.ini <- ggplot2::ggplot_build(eval(parse(text = paste(paste(paste0(tempo.gg.name, 1:tempo.gg.count), collapse = " + "), if( ! is.null(stat.disp)){' + ggplot2::geom_text(data = tempo.data.max, mapping = ggplot2::aes_string(x = 1, y = y, label = "label"), size = stat.size, color = "black", angle = stat.angle, hjust = stat.just$hjust, vjust = stat.just$vjust)'})))) # added here to have room for annotation
dot.coord <- tempo.graph.info.ini$data[[1]]
dot.coord$x <- as.numeric(dot.coord$x) # because weird class
dot.coord$PANEL <- as.numeric(dot.coord$PANEL) # because numbers as levels. But may be a problem is facet are reordered ?
@@ -9698,8 +9706,8 @@ mapping = ggplot2::aes_string(x = "X", y = "Y", label = ifelse(stat.disp.mean ==
size = stat.size,
color = "black",
angle = stat.angle,
-hjust = ifelse(vertical == TRUE, 0.5, 1.1),
-vjust = ifelse(vertical == TRUE, 1.1, 0.5)
+hjust = stat.just$hjust,
+vjust = stat.just$vjust
)) # stat$X used here because identical to stat.nolog but has the X. WARNING: no need of order() for labels because box.coord$x set the order. For justification, see https://stackoverflow.com/questions/7263849/what-do-hjust-and-vjust-do-when-making-a-plot-using-ggplot
coord.names <- c(coord.names, "stat.display")
}else if(stat.disp == "above"){
@@ -9763,6 +9771,9 @@ tempo.center.ref <- "MEAN"
# tempo.log.low <- if(diff(y.lim) > 0){stat.coord3[, tempo.center.ref] < 0}else{stat.coord3[, tempo.center.ref] >= 0}
# stat.coord3$Y[tempo.log.high] <- stat.coord3[tempo.log.high, tempo.high.ref]
# stat.coord3$Y[tempo.log.low] <- stat.coord3[tempo.log.low, tempo.low.ref]
+# add distance
+stat.coord3$Y <- stat.coord3$Y + diff(y.lim) * stat.dist / 100
+# end add distance
# correct median or mean text format
if(y.log != "no"){
stat.coord3[, tempo.center.ref] <- ifelse(y.log == "log2", 2, 10)^(stat.coord3[, tempo.center.ref])
@@ -9777,10 +9788,10 @@ mapping = ggplot2::aes_string(x = "x", y = "Y", label = tempo.center.ref),
size = stat.size,
color = "black",
angle = stat.angle,
-hjust = ifelse(vertical == TRUE, stat.just$hjust, stat.just$hjust - stat.dist),
-vjust = ifelse(vertical == TRUE, stat.just$vjust - stat.dist, stat.just$vjust)
+hjust = stat.just$hjust,
+vjust = stat.just$vjust
)) # WARNING: no need of order() for labels because box.coord$x set the order
-coord.names <- c(coord.names, "stat.display.positive")
+coord.names <- c(coord.names, "stat.display")
# }
# if(any(tempo.log.low) == TRUE){
# tempo.stat <- stat.coord3[tempo.log.low,]
diff --git a/fun_gg_boxplot.docx b/fun_gg_boxplot.docx
index 7612714fb04a1a0af032b5e91ce7d01a39a25d07..fa25d301a30f1a5b17a30eed6d7dc033a048064b 100644
Binary files a/fun_gg_boxplot.docx and b/fun_gg_boxplot.docx differ