Commit 0719a94d authored by Gael's avatar Gael
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justification and distance fixed for fun_gg_boxplot(), README improved

parent 21fca3f4
#### 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 |
| --- | --- |
| [![R Version](https://img.shields.io/badge/code-R-blue?style=plastic)](https://cran.r-project.org/mirrors.html) | [![Dependencies: R Version](https://img.shields.io/badge/R-v4.0.2-blue?style=plastic)](https://cran.r-project.org/mirrors.html) |
| [![License: GPL-3.0](https://img.shields.io/badge/licence-GPL%20(%3E%3D3)-green?style=plastic)](https://www.gnu.org/licenses) | [![Dependencies: R Package](https://img.shields.io/badge/package-car%20v3.0.9-blue?style=plastic)](http://www.rforge.net/car/) |
| | [![Dependencies: R Package](https://img.shields.io/badge/package-carData%20v3.0.4-blue?style=plastic)](http://www.rforge.net/carData/) |
| | [![Dependencies: R Package](https://img.shields.io/badge/package-emmeans%20v1.5.0-blue?style=plastic)](http://www.rforge.net/emmeans/) |
| | [![Dependencies: R Package](https://img.shields.io/badge/package-ggplot2%20v3.3.2-blue?style=plastic)](https://github.com/tidyverse/ggplot2) |
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| | [![Dependencies: R Package](https://img.shields.io/badge/package-lmerTest%20v3.1.2-blue?style=plastic)](http://www.rforge.net/lmerTest/) |
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| | [![Dependencies: R Package](https://img.shields.io/badge/package-Matrix%20v1.2.18-blue?style=plastic)](http://www.rforge.net/Matrix/) |
| | [![Dependencies: R Package](https://img.shields.io/badge/toolbox-cute%20little%20R%20functions%20v6.0.0-blue?style=plastic)](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 Set of functions that facilitate basic procedures in 1) object analysis, 2) object modification, 3) graphic handling and 4) log file management.
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
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 ## REPOSITORY CONTENT
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
## 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 **cute_little_R_functions.docx** same as cute_little_R_functions.R but for better reading (interactive outline at the beginning of the file)
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
**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 ## DESCRIPTIONS OF THE FUNCTIONS
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
| 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 | Graphics management | |
fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation | --- | --- |
| **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 | Graphic extraction | |
fun_python_pack_import() #### check if python packages are present | --- | --- |
| **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.
1) Select the desired tagged release
2) Browse files
#### CREDITS 3) Display the cute_little_R_functions.R as raw file
Gael A. Millot, Hub-C3BI, Institut Pasteur, USR 3756 IP CNRS, Paris, France 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")
`
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).
#### HOW TO USE IT Or in the R/RStudio console, type the name of the function without brackets. Example : `fun_info`.
1) Download the desired Tagged version, never the current master, at https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/tags
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") ## VERSIONS
Description of the functions is at the beginning of the function body. To obtain it: The different releases are tagged [here](https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/tags)
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.
## 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.
#### FILE DESCRIPTIONS
cute_little_R_functions.R file that has to be sourced ## CITATION
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
Not yet published
## CREDITS
#### WEB LOCATION [Gael A. Millot](https://gitlab.pasteur.fr/gmillot), Hub-CBD, Institut Pasteur, USR 3756 IP CNRS, Paris, France
Check for updated versions (most recent tags) at https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/tags
## ACKNOWLEDGEMENTS
R and R packages developers
Gitlab developers
#### WHAT'S NEW IN
## WHAT'S NEW IN
## v6.0.0 ### v6.0.0
1) name of functions changed: 1) name of functions changed:
fun_param_check() fun_check() fun_param_check() fun_check()
fun_object_info() fun_info() fun_object_info() fun_info()
fun_1D_comp() fun_comp_1d() fun_1D_comp() fun_comp_1d()
fun_2D_comp() fun_comp_2d() fun_2D_comp() fun_comp_2d()
fun_list_comp() fun_comp_list() fun_list_comp() fun_comp_list()
fun_2D_head() fun_head() fun_2D_head() fun_head()
fun_2D_tail() fun_tail() fun_2D_tail() fun_tail()
fun_dataframe_remodeling() fun_df_remod() fun_dataframe_remodeling() fun_df_remod()
fun_by_case_matrix_op() fun_mat_op() fun_by_case_matrix_op() fun_mat_op()
fun_rounding() fun_round() fun_rounding() fun_round()
fun_90clock_matrix_rot() fun_mat_rotate() fun_90clock_matrix_rot() fun_mat_rotate()
fun_hexa_hsv_color_matrix() fun_mat_num2color() fun_hexa_hsv_color_matrix() fun_mat_num2color()
fun_graph_param_prior_plot() fun_prior_plot() fun_graph_param_prior_plot() fun_prior_plot()
fun_feature_post_plot() fun_post_plot() fun_feature_post_plot() fun_post_plot()
fun_window_width_resizing() fun_width() fun_window_width_resizing() fun_width()
fun_open_window() fun_open() fun_open_window() fun_open()
fun_close_specif_window() fun_close() fun_close_specif_window() fun_close()
fun_var_trim_display() fun_trim() fun_var_trim_display() fun_trim()
fun_export_data() fun_report() fun_export_data() fun_report()
2) new functions added: 2) new functions added:
fun_name_change() fun_name_change()
fun_mat_fill() fun_mat_fill()
fun_permut() fun_permut()
fun_permut_consec() fun_permut_consec()
fun_empty_graph() fun_empty_graph()
fun_gg_palette() fun_gg_palette()
fun_gg_just() fun_gg_just()
fun_gg_point_rast() fun_gg_point_rast()
fun_gg_scatter() fun_gg_scatter()
fun_gg_bar()
fun_gg_heatmap()
fun_gg_empty_graph() fun_gg_empty_graph()
fun_segmentation() fun_segmentation()
fun_pack() fun_pack()
fun_python_pack() fun_python_pack()
fun_warning() 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 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 4) in fun_param_check(): (1) has now the class = "vector", (2) argument fun.name added
...@@ -178,69 +262,72 @@ fun_warning() ...@@ -178,69 +262,72 @@ fun_warning()
6) Functions checked for R version 3.6.1 6) Functions checked for R version 3.6.1
7) function deprecated: 7) function deprecated:
fun_refactorization() fun_refactorization()
## v5.1.0 ### v5.1.0
1) bugs corrected in fun_2D_head() and fun_2D_tail() functions 1) bugs corrected in fun_2D_head() and fun_2D_tail() functions
## v5.0.0 ### v5.0.0
1) fun_2D_head() function added 1) fun_2D_head() function added
2) fun_2D_tail() function added 2) fun_2D_tail() function added
3) argument "noquote" added in fun_export_data() 3) argument "noquote" added in fun_export_data()
## v4.9.0 ### v4.9.0
1) fun_mat_inv() function added 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 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 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 1) fun_by_case_matrix_op() added
## v4.5.0 ### v4.5.0
1) fun_open_window() improved to deal with Linux systems 1) fun_open_window() improved to deal with Linux systems
2) fun_graph_param_prior_plot() 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) 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" 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 1) bug in the fun_2D_comp() function fixed
## v4.1.0 ### v4.1.0
1) text.corner replaced by corner.text everywhere 1) text.corner replaced by corner.text everywhere
## v4.0.0 ### v4.0.0
1) fun_var_trim_display() function added 1) fun_var_trim_display() function added
...@@ -251,14 +338,14 @@ fun_refactorization() ...@@ -251,14 +338,14 @@ fun_refactorization()
4) error messages now mention the function that generates this message 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 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 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 1) cute_little_functions.R renamed cute_little_R_functions.R
...@@ -267,12 +354,12 @@ fun_refactorization() ...@@ -267,12 +354,12 @@ fun_refactorization()
3) more examples added, also draws added in the .docx file for fun_dataframe_remodeling() 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 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 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() ...@@ -281,7 +368,13 @@ fun_refactorization()
3) Bug corrected in fun_refactorization() function 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 1) fun_1D_comp() function improved: provide the common elements, common names and common levels if exist
......
...@@ -7966,7 +7966,6 @@ return(output) # do not use cat() because the idea is to reuse the message ...@@ -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 # check s/lapply everywhere with get: done cute boxplot scatter
# get() with env everywhere: 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 # add the new NA and NULL check cute, boxplot, scatter: done boxplot, scatter
...@@ -8011,7 +8010,7 @@ y.bottom.extra.margin = 0.05, ...@@ -8011,7 +8010,7 @@ y.bottom.extra.margin = 0.05,
stat.disp = "top", stat.disp = "top",
stat.disp.mean = FALSE, stat.disp.mean = FALSE,
stat.size = 4, stat.size = 4,
stat.dist = 2, stat.dist = 5,
stat.angle = 0, stat.angle = 0,
vertical = TRUE, vertical = TRUE,
text.size = 12, text.size = 12,
...@@ -8091,7 +8090,7 @@ lib.path = NULL ...@@ -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: 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.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.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. # 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) # 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) # 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 ...@@ -8142,8 +8141,7 @@ lib.path = NULL
# $sup.whisker.edge: coordinates of top whisker edges (x and xend) # $sup.whisker.edge: coordinates of top whisker edges (x and xend)
# $inf.whisker.edge: coordinates of bottom 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) # $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: coordinates of stat numbers (only if stat.disp argument is not NULL)
# $stat.display.negative: coordinates of stat numbers when negative (only if stat.disp argument is TRUE)
# 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.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") # 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 # $panel: the variable names used for the panels (NULL if no panels). WARNING: NA can be present according to ggplot2 upgrade to v3.3.0
...@@ -8155,7 +8153,7 @@ lib.path = NULL ...@@ -8155,7 +8153,7 @@ lib.path = NULL
# DEBUGGING # DEBUGGING
# set.seed(1) ; obs1 <- data.frame(Time = c(rnorm(10), rnorm(10) + 2), Categ1 = rep(c("G", "H"), each = 10), stringsAsFactors = TRUE) ; set.seed(NULL) ; obs1$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), 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), 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