README.md 11.8 KB
Newer Older
1
2
3
4
5
6
[//]: # "#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) |
7
| [![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-Cairo%20v1.5_12.2-blue?style=plastic)](https://cran.r-project.org/web/packages/Cairo/index.html) |
8
9
|  | [![Dependencies: R Package](https://img.shields.io/badge/package-ggplot2%20v3.3.2-blue?style=plastic)](https://github.com/tidyverse/ggplot2) |
|  | [![Dependencies: R Package](https://img.shields.io/badge/package-lubridate%20v1.7.9-blue?style=plastic)](https://github.com/tidyverse/lubridate) |
10
11
12
|  | [![Dependencies: R Package](https://img.shields.io/badge/package-reshape2%20v1.4.4-blue?style=plastic)](https://cran.r-project.org/web/packages/reshape2/index.html) |
|  | [![Dependencies: R Package](https://img.shields.io/badge/package-reticulate%20v1.16-blue?style=plastic)](https://cran.r-project.org/web/packages/reticulate/index.html)|
|  | [![Dependencies: R Package](https://img.shields.io/badge/package-scales%20v1.1.1-blue?style=plastic)](https://cran.r-project.org/web/packages/scales/index.html) |
13
14
15
16
17
18
19
20
21
22
23
24
25
26


## 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)
Gael  MILLOT's avatar
Gael MILLOT committed
27

Gael  MILLOT's avatar
Gael MILLOT committed
28

29
## AIM
Gael  MILLOT's avatar
Gael MILLOT committed
30

Gael  MILLOT's avatar
Gael MILLOT committed
31

32
Set of functions that facilitate basic procedures in 1) object analysis, 2) object modification, 3) graphic handling and 4) log file management.
Gael  MILLOT's avatar
Gael MILLOT committed
33

34
The present repository of Cute Little R functions is for beta testing. Ultimately, functions will be provided as packages
Gael  MILLOT's avatar
Gael MILLOT committed
35
36


37
## REPOSITORY CONTENT
Gael  MILLOT's avatar
Gael MILLOT committed
38

39
**cute_little_R_functions.R** file that has to be sourced in R or RStudio
Gael  MILLOT's avatar
Gael MILLOT committed
40

41
**cute_little_R_functions.docx** same as cute_little_R_functions.R but for better reading (interactive outline at the beginning of the file)
Gael  MILLOT's avatar
Gael MILLOT committed
42

43
44
45
46
**fun_gg_boxplot.docx** for better reading of the argument description

**fun_gg_scatter.docx** for better reading of the argument description

47
**examples.R** examples of all the functions, except fun_gg_boxplot() and fun_gg_scatter(), that can be sourced or copied-pasted
Gael  MILLOT's avatar
Gael MILLOT committed
48

49
**examples_gg_boxplot.R** examples of fun_gg_boxplot() that can be sourced or copied-pasted
Gael  MILLOT's avatar
Gael MILLOT committed
50

51
**examples_gg_scatter.R** examples of fun_gg_scatter() that can be sourced or copied-pasted
Gael  MILLOT's avatar
Gael MILLOT committed
52

53
**other** folder containing avorted developments
Gael  MILLOT's avatar
Gael MILLOT committed
54
55


56
## DESCRIPTIONS OF THE FUNCTIONS
Gael  MILLOT's avatar
Gael MILLOT committed
57

58
59
| Object analysis | |
| --- | --- |
Gael's avatar
Gael committed
60
61
62
| **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 |
63
64
| **fun_head()** | head of the corners of big 2D objects |
| **fun_tail()** | tail of the corners of big 2D objects |
Gael's avatar
Gael committed
65
| **fun_comp_1d()** | comparison of two 1D datasets (vectors, factors, 1D tables) |
66
| **fun_comp_2d()** | comparison of two 2D datasets (matrices, data.drames, tables) |
Gael's avatar
Gael committed
67
68
| **fun_comp_list()** | comparison of two lists |
| **fun_test()** | test combinations of argument values of a function and return errors (and graphs) |
Gael  MILLOT's avatar
Gael MILLOT committed
69

70
71
| Object modification | |
| --- | --- |
Gael's avatar
Gael committed
72
| **fun_name_change()** | check a vector of character strings and modify any string if present in another vector |
73
74
| **fun_df_remod()** | remodel a data frame to have column name as a qualitative values and vice-versa |
| **fun_round()** | round numbers if decimals present |
Gael's avatar
Gael committed
75
76
77
78
79
| **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 |
80
| **fun_permut()** | progressively break a vector order |
Gael's avatar
Gael committed
81
| **fun_slide()** | return a computation made on a vector using a sliding window |
Gael  MILLOT's avatar
Gael MILLOT committed
82

83
84
| Graphics management | |
| --- | --- |
85
86
87
88
| **fun_width()** | graphic device width depending on the number of classes to plot |
| **fun_open()** | open a GUI or pdf graphic device |
| **fun_prior_plot()** | set graphic parameters before plotting (erase axes for instance) |
| **fun_scale()** | select nice labeling numbers when setting the number of ticks on an axis |
Gael's avatar
Gael committed
89
| **fun_inter_ticks()** | define coordinates of secondary ticks |
90
91
| **fun_post_plot()** | set graphic parameters after plotting (axes redesign for instance) |
| **fun_close()** | close specific graphic devices |
Gael  MILLOT's avatar
Gael MILLOT committed
92

93
94
| Standard graphics | |
| --- | --- |
95
| **fun_empty_graph()** | generate an empty graphic device with text in the middle |
Gael  MILLOT's avatar
Gael MILLOT committed
96

97
98
| gg graphics | |
| --- | --- |
99
| **fun_gg_palette()** | select colors on the ggplot2 default color palette |
100
| **fun_gg_just()** | ggplot2 justification of annotated text or axis labeling, depending on angle |
Gael's avatar
Gael committed
101
102
| **fun_gg_get_legend()** | get the legend of ggplot objects |
| **fun_gg_point_rast()** | ggplot2 raster scatterplot layer |
103
| **fun_gg_boxplot()** | ggplot2 boxplot + dots + means + median/mean values |
Gael's avatar
Gael committed
104
| **fun_gg_scatter()** | ggplot2 scatterplot + lines (up to 6 overlays totally) |
105
| **fun_gg_empty_graph()** | generate an empty graphic device with text in the middle |
Gael  MILLOT's avatar
Gael MILLOT committed
106

107
108
| Graphic extraction | |
| --- | --- |
Gael's avatar
Gael committed
109
110
| **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 |
Gael  MILLOT's avatar
Gael MILLOT committed
111

112
113
| Import | |
| --- | --- |
Gael's avatar
Gael committed
114
115
| **fun_pack()** | check if R packages are present and import into the working environment |
| **fun_python_pack()** | check if python packages are present |
Gael  MILLOT's avatar
Gael MILLOT committed
116

117
118
| Print / Exporting results (text & tables) | |
| --- | --- |
119
120
| **fun_report()** | print strings or results into a log file |
| **fun_get_message()** | catch the error/warning/other messages of an evaluated expression |
Gael  MILLOT's avatar
Gael MILLOT committed
121
122


123
## HOW TO LOAD AND MANIPULATE cute_little_R_functions
Gael  MILLOT's avatar
Gael MILLOT committed
124
125


126
Download the desired Tagged version, never the current master, at https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/tags
Gael  MILLOT's avatar
Gael MILLOT committed
127

Gael's avatar
Gael committed
128
For that:
Gael  MILLOT's avatar
Gael MILLOT committed
129

Gael's avatar
Gael committed
130
1) Select the desired tagged release
Gael  MILLOT's avatar
Gael MILLOT committed
131

Gael's avatar
Gael committed
132
133
134
135
136
137
2) Browse files

3) Display the cute_little_R_functions.R as raw file

4) Source the file using the url address. Example:

138
`  source("https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/557976d693e37b499b89c76e4b2142846eb89d5b/cute_little_R_functions.R")  `
Gael  MILLOT's avatar
Gael MILLOT committed
139

140
Complete description of each function is at the beginning of the function body. To obtain it:
Gael  MILLOT's avatar
Gael MILLOT committed
141

142
1) Either use the cute_little_R_functions.docx.
Gael's avatar
Gael committed
143
144

2) Or in the R/RStudio console, type the name of the function without brackets. Example : `fun_info`.
Gael  MILLOT's avatar
Gael MILLOT committed
145
146


147
## VERSIONS
Gael  MILLOT's avatar
Gael MILLOT committed
148

149
The different releases are tagged [here](https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/tags)
Gael  MILLOT's avatar
Gael MILLOT committed
150

Gael  MILLOT's avatar
Gael MILLOT committed
151

152
## LICENCE
Gael  MILLOT's avatar
Gael MILLOT committed
153

154
155
156
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.
Gael  MILLOT's avatar
Gael MILLOT committed
157

Gael  MILLOT's avatar
Gael MILLOT committed
158

159
## CITATION
Gael  MILLOT's avatar
Gael MILLOT committed
160

161
Not yet published
Gael  MILLOT's avatar
Gael MILLOT committed
162
163


164
## CREDITS
Gael  MILLOT's avatar
Gael MILLOT committed
165

166
[Gael A. Millot](https://gitlab.pasteur.fr/gmillot), Hub-CBD, Institut Pasteur, USR 3756 IP CNRS, Paris, France
Gael  MILLOT's avatar
Gael MILLOT committed
167
168


169
## ACKNOWLEDGEMENTS
Gael  MILLOT's avatar
Gael MILLOT committed
170

171
R and R packages developers
Gael  MILLOT's avatar
Gael MILLOT committed
172

173
174
175
176
177
Gitlab developers


## WHAT'S NEW IN

Gael's avatar
Gael committed
178
179
180
181
182
183
184
### v8.0.0

1) Examples improved

2) Some functions debugged


185
186
187
188
189
### v7.0.0

1) Upgrade to R-4.0.2, among other things


190
### v6.0.0
Gael  MILLOT's avatar
Gael MILLOT committed
191
192

1) name of functions changed:
193

Gael  MILLOT's avatar
Gael MILLOT committed
194
fun_param_check()	fun_check()
195

Gael  MILLOT's avatar
Gael MILLOT committed
196
fun_object_info()	fun_info()
197

Gael  MILLOT's avatar
saving    
Gael MILLOT committed
198
fun_1D_comp()	fun_comp_1d()
199

Gael  MILLOT's avatar
saving    
Gael MILLOT committed
200
fun_2D_comp()	fun_comp_2d()
201

Gael  MILLOT's avatar
saving    
Gael MILLOT committed
202
fun_list_comp()	fun_comp_list()
203

Gael  MILLOT's avatar
saving    
Gael MILLOT committed
204
fun_2D_head()	fun_head()
205

Gael  MILLOT's avatar
saving    
Gael MILLOT committed
206
fun_2D_tail()	fun_tail()
207

Gael  MILLOT's avatar
Gael MILLOT committed
208
fun_dataframe_remodeling()	fun_df_remod()
209

Gael  MILLOT's avatar
Gael MILLOT committed
210
fun_by_case_matrix_op()	fun_mat_op()
211

Gael  MILLOT's avatar
Gael MILLOT committed
212
fun_rounding()	fun_round()
213

214
fun_90clock_matrix_rot()	fun_mat_rotate()
215

216
fun_hexa_hsv_color_matrix()	fun_mat_num2color()
217

Gael  MILLOT's avatar
Gael MILLOT committed
218
fun_graph_param_prior_plot()	fun_prior_plot()
219

Gael  MILLOT's avatar
Gael MILLOT committed
220
fun_feature_post_plot()	fun_post_plot()
221

Gael  MILLOT's avatar
Gael MILLOT committed
222
fun_window_width_resizing()	fun_width()
223

Gael  MILLOT's avatar
Gael MILLOT committed
224
fun_open_window()	fun_open()
225

Gael  MILLOT's avatar
Gael MILLOT committed
226
fun_close_specif_window()	fun_close()
227

Gael  MILLOT's avatar
Gael MILLOT committed
228
fun_var_trim_display()	fun_trim()
229

Gael  MILLOT's avatar
Gael MILLOT committed
230
fun_export_data()	fun_report()
Gael  MILLOT's avatar
Gael MILLOT committed
231

232
233


Gael  MILLOT's avatar
Gael MILLOT committed
234
2) new functions added:
235

Gael  MILLOT's avatar
Gael MILLOT committed
236
fun_name_change()
237

Gael  MILLOT's avatar
Gael MILLOT committed
238
fun_mat_fill()
239

240
fun_permut()
241

Gael  MILLOT's avatar
Gael MILLOT committed
242
fun_permut_consec()
243

Gael  MILLOT's avatar
Gael MILLOT committed
244
fun_empty_graph()
245

Gael  MILLOT's avatar
Gael MILLOT committed
246
fun_gg_palette()
247

Gael  MILLOT's avatar
Gael MILLOT committed
248
fun_gg_just()
249

Gael  MILLOT's avatar
saving    
Gael MILLOT committed
250
fun_gg_point_rast()
251

Gael  MILLOT's avatar
Gael MILLOT committed
252
fun_gg_scatter()
253

Gael  MILLOT's avatar
Gael MILLOT committed
254
fun_gg_empty_graph()
255

Gael  MILLOT's avatar
Gael MILLOT committed
256
fun_segmentation()
257

Gael  MILLOT's avatar
Gael MILLOT committed
258
fun_pack()
259

Gael  MILLOT's avatar
Gael MILLOT committed
260
fun_python_pack()
261

Gael  MILLOT's avatar
Gael MILLOT committed
262
fun_warning()
Gael  MILLOT's avatar
Gael MILLOT committed
263

264
265


Gael  MILLOT's avatar
saving    
Gael MILLOT committed
266
3) text error modified in fun_head() and fun_tail(), + deals without all objects but use head() and tail() if not 2D object
Gael  MILLOT's avatar
Gael MILLOT committed
267
268
269

4) in fun_param_check(): (1) has now the class = "vector", (2) argument fun.name added

Gael  MILLOT's avatar
Gael MILLOT committed
270
271
5) writting and debugging message errors improved in all the functions

Gael  MILLOT's avatar
Gael MILLOT committed
272
273
274
6) Functions checked for R version 3.6.1

7) function deprecated:
275

Gael  MILLOT's avatar
Gael MILLOT committed
276
fun_refactorization()
Gael  MILLOT's avatar
Gael MILLOT committed
277
278


279
### v5.1.0
Gael  MILLOT's avatar
Gael MILLOT committed
280
281
282
283

1) bugs corrected in fun_2D_head() and fun_2D_tail() functions


284
### v5.0.0
Gael  MILLOT's avatar
Gael MILLOT committed
285
286

1) fun_2D_head() function added
287

Gael  MILLOT's avatar
Gael MILLOT committed
288
2) fun_2D_tail() function added
289

Gael  MILLOT's avatar
Gael MILLOT committed
290
291
292
3) argument "noquote" added in fun_export_data()


293
### v4.9.0
Gael  MILLOT's avatar
Gael MILLOT committed
294
295
296
297

1) fun_mat_inv() function added


298
### v4.8.0
Gael  MILLOT's avatar
Gael MILLOT committed
299
300
301
302

1) magnific argument removed in fun_feature_post_plot() because no need anymore


303
### v4.7.0
Gael  MILLOT's avatar
Gael MILLOT committed
304
305
306
307

1) check of numeric arguments: class = "numeric" -> mode = "numeric" to allow for integers values in these arguments


308
### v4.6.0
Gael  MILLOT's avatar
Gael MILLOT committed
309
310
311
312

1) fun_by_case_matrix_op() added


313
### v4.5.0
Gael  MILLOT's avatar
Gael MILLOT committed
314
315
316
317
318
319

1) fun_open_window() improved to deal with Linux systems

2) fun_graph_param_prior_plot() improved to deal with Linux systems


320
### v4.4.0
Gael  MILLOT's avatar
Gael MILLOT committed
321
322
323
324

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)


325
### v4.3.0
Gael  MILLOT's avatar
Gael MILLOT committed
326
327
328
329

1) fun_object_info() now manages object class "ordered" "factor"


330
### v4.2.0
Gael  MILLOT's avatar
Gael MILLOT committed
331
332
333
334

1) bug in the fun_2D_comp() function fixed


335
### v4.1.0
Gael  MILLOT's avatar
Gael MILLOT committed
336
337
338
339

1) text.corner replaced by corner.text everywhere


340
### v4.0.0
Gael  MILLOT's avatar
Gael MILLOT committed
341
342
343
344
345
346
347
348
349
350

1) fun_var_trim_display() function added

2) fun_feature_post_plot() function now provides additional coordinates when there are margins between the figure region and the device region

3) fun_2D_comp() function now provide the common row and column names, and a bug fixed in the detection of identical row or column content

4) error messages now mention the function that generates this message 


351
### v3.1.0
Gael  MILLOT's avatar
Gael MILLOT committed
352
353
354
355
356
357

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


358
### v3.0.0
Gael  MILLOT's avatar
Gael MILLOT committed
359

Gael  MILLOT's avatar
Gael MILLOT committed
360
1) cute_little_functions.R renamed cute_little_R_functions.R
Gael  MILLOT's avatar
Gael MILLOT committed
361

Gael  MILLOT's avatar
Gael MILLOT committed
362
363
2) function fun_dataframe_flipping() has been renamed fun_dataframe_remodeling()

Gael  MILLOT's avatar
Gael MILLOT committed
364
3) more examples added, also draws added in the .docx file for fun_dataframe_remodeling()
Gael  MILLOT's avatar
Gael MILLOT committed
365
366


367
### v2.0.1
Gael  MILLOT's avatar
Gael MILLOT committed
368
369
370
371

1) functions that use other functions from this toolset now check if these required functions are indeed present in the R environment


372
### v2.0.0
Gael  MILLOT's avatar
Gael MILLOT committed
373
374
375
376
377
378
379
380

1) fun_feature_post_plot() function improved: Now independent magnification for x axis/labels and y axis/labels. BEWARE: argument names have been modified

2) Bug corrected in fun_graph_param_prior_plot() function

3) Bug corrected in fun_refactorization() function


381
382
### v1.3

Gael  MILLOT's avatar
Gael MILLOT committed
383
1) fun_1D_comp() function improved: provide the common elements, common names and common levels if exist
Gael  MILLOT's avatar
Gael MILLOT committed
384
385


Gael's avatar
Gael committed
386
387
388
### v1

Everything