README.md 7.31 KB
Newer Older
Gael  MILLOT's avatar
Gael MILLOT committed
1
2
#### DESCRIPTION

Gael  MILLOT's avatar
Gael MILLOT committed
3
Cute Little R Functions contains 34 functions for R/RStudio 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
4

Gael  MILLOT's avatar
Gael MILLOT committed
5
The function names are:
Gael  MILLOT's avatar
Gael MILLOT committed
6

Gael  MILLOT's avatar
Gael MILLOT committed
7
8
## Object analysis

Gael  MILLOT's avatar
Gael MILLOT committed
9
10
fun_param_check() #### checking class, type, length, etc. of objects
fun_object_info() #### recovering object information
Gael  MILLOT's avatar
Gael MILLOT committed
11
12
13
14
15
16
17
18
19
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


## Object modification

Gael  MILLOT's avatar
Gael MILLOT committed
20
fun_name_change() #### check a vector of character strings and modify any string if present in another vector
Gael  MILLOT's avatar
Gael MILLOT committed
21
22
23
24
25
26
27
28
29
30
31
32
33
34
fun_dataframe_remodeling() #### remodeling a data frame to have column name as a qualitative column 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() #### Conversion of a numeric matrix into hexadecimal color matrix
fun_by_case_matrix_op() #### assembling of 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_consec_pos_perm() #### progressively breaks a vector order


## Graphics management

fun_window_width_resizing() #### window width depending on classes to plot
Gael  MILLOT's avatar
Gael MILLOT committed
35
36
37
38
fun_open_window() #### open a GUI or pdf graphic window
fun_prior_plot() #### graph param before plotting
fun_post_plot() #### graph param after plotting
fun_close_specif_window() #### closing specific graphic windows
Gael  MILLOT's avatar
Gael MILLOT committed
39
40
41
42
43
44
45
46
47
48


## Standard graphics

fun_empty_graph() #### text to display for empty graphs


## gg graphics

fun_gg_palette() #### ggplot2 default color palette
Gael  MILLOT's avatar
Gael MILLOT committed
49
fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle
Gael  MILLOT's avatar
Gael MILLOT committed
50
51
52
53
54
55
56
57
fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally)
fun_gg_bar_mean() #### ggplot2 mean barplot + overlaid dots if required
fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required
fun_gg_empty_graph() #### text to display for empty graphs


## Graphic extraction

Gael  MILLOT's avatar
Gael MILLOT committed
58
59
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
Gael  MILLOT's avatar
Gael MILLOT committed
60
61
62
63


## Import

Gael  MILLOT's avatar
Gael MILLOT committed
64
65
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
Gael  MILLOT's avatar
Gael MILLOT committed
66
67
68
69


## Exporting results (text & tables)

Gael  MILLOT's avatar
Gael MILLOT committed
70
fun_export_data() #### print string or data object into output file
Gael  MILLOT's avatar
Gael MILLOT committed
71

Gael  MILLOT's avatar
Gael MILLOT committed
72
73


Gael  MILLOT's avatar
Gael MILLOT committed
74
75
76
77
78
79
80
81
82
83
84
85
#### 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 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


Gael  MILLOT's avatar
Gael MILLOT committed
86
87
#### HOW TO USE IT

Gael  MILLOT's avatar
Gael MILLOT committed
88
89
Download the desired Tagged version, never the current master.

Gael  MILLOT's avatar
Gael MILLOT committed
90
Source the cute_little_R_functions.R into R/RStudio to have the functions available in the working environment.
Gael  MILLOT's avatar
Gael MILLOT committed
91

Gael  MILLOT's avatar
Gael MILLOT committed
92
Description of the functions is at the beginning of the function body. To obtain it:
Gael  MILLOT's avatar
Gael MILLOT committed
93

Gael  MILLOT's avatar
Gael MILLOT committed
94
	Either read the cute_little_functions.docx (or open the cute_little_R_functions.R file).
Gael  MILLOT's avatar
Gael MILLOT committed
95
	
Gael  MILLOT's avatar
Gael MILLOT committed
96
	Or in the R/RStudio console, type the name of the function without brackets. Example : fun_object_info.
Gael  MILLOT's avatar
Gael MILLOT committed
97
98


Gael  MILLOT's avatar
Gael MILLOT committed
99
#### FILE DESCRIPTIONS
Gael  MILLOT's avatar
Gael MILLOT committed
100

Gael  MILLOT's avatar
Gael MILLOT committed
101
102
cute_little_R_functions.R	file that has to be sourced
cute_little_R_functions.docx	just for easier code reading
Gael  MILLOT's avatar
Gael MILLOT committed
103
examples_alone.txt	compile all the examples of the functions into a single file
Gael  MILLOT's avatar
Gael MILLOT committed
104
105
106
107


#### WEB LOCATION

Gael  MILLOT's avatar
Gael MILLOT committed
108
Check for updated versions (most recent tags) at https://gitlab.pasteur.fr/gmillot/cute_little_functions/tags
Gael  MILLOT's avatar
Gael MILLOT committed
109
110


Gael  MILLOT's avatar
Gael MILLOT committed
111
#### WHAT'S NEW IN
Gael  MILLOT's avatar
Gael MILLOT committed
112

Gael  MILLOT's avatar
Gael MILLOT committed
113
114
115
116
117
118
119
120
121
122

## v6.0.0

1) name of functions changed:
fun_rounding()	fun_round()
fun_hexa_hsv_color_matrix()	fun_num2color_mat()
fun_graph_param_prior_plot()	fun_prior_plot()
fun_feature_post_plot()	fun_post_plot()

2) new functions added:
Gael  MILLOT's avatar
Gael MILLOT committed
123
fun_name_change()
Gael  MILLOT's avatar
Gael MILLOT committed
124
125
126
127
fun_mat_fill()
fun_consec_pos_perm()
fun_empty_graph()
fun_gg_palette()
Gael  MILLOT's avatar
Gael MILLOT committed
128
fun_gg_just()
Gael  MILLOT's avatar
Gael MILLOT committed
129
130
131
132
133
134
135
136
137
138
139
140
fun_gg_scatter()
fun_gg_bar_mean()
fun_gg_heatmap()
fun_gg_empty_graph()
fun_segmentation()
fun_pack_import()
fun_python_pack_import()

3) text error modified in fun_2D_head() and fun_2D_tail()

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

Gael  MILLOT's avatar
Gael MILLOT committed
141
142
143
5) writting and debugging message errors improved in all the functions

6) Functions checked for R version 3.5.3
Gael  MILLOT's avatar
Gael MILLOT committed
144
145


Gael  MILLOT's avatar
Gael MILLOT committed
146
147
148
149
150
## v5.1.0

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


Gael  MILLOT's avatar
Gael MILLOT committed
151
152
153
154
155
156
157
## v5.0.0

1) fun_2D_head() function added
2) fun_2D_tail() function added
3) argument "noquote" added in fun_export_data()


Gael  MILLOT's avatar
Gael MILLOT committed
158
159
160
161
162
## v4.9.0

1) fun_mat_inv() function added


Gael  MILLOT's avatar
Gael MILLOT committed
163
164
165
166
167
## v4.8.0

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


Gael  MILLOT's avatar
Gael MILLOT committed
168
169
170
171
172
## v4.7.0

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


Gael  MILLOT's avatar
Gael MILLOT committed
173
174
175
176
177
## v4.6.0

1) fun_by_case_matrix_op() added


Gael  MILLOT's avatar
Gael MILLOT committed
178
179
180
181
182
183
184
## 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


Gael  MILLOT's avatar
Gael MILLOT committed
185
186
187
188
189
## 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)


Gael  MILLOT's avatar
Gael MILLOT committed
190
191
192
193
194
## v4.3.0

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


Gael  MILLOT's avatar
Gael MILLOT committed
195
196
197
198
199
## v4.2.0

1) bug in the fun_2D_comp() function fixed


Gael  MILLOT's avatar
Gael MILLOT committed
200
201
202
203
204
## v4.1.0

1) text.corner replaced by corner.text everywhere


Gael  MILLOT's avatar
Gael MILLOT committed
205
206
207
208
209
210
211
212
213
214
215
## v4.0.0

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 


Gael  MILLOT's avatar
Gael MILLOT committed
216
217
218
219
220
221
222
## 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


Gael  MILLOT's avatar
Gael MILLOT committed
223
224
## v3.0.0

Gael  MILLOT's avatar
Gael MILLOT committed
225
1) cute_little_functions.R renamed cute_little_R_functions.R
Gael  MILLOT's avatar
Gael MILLOT committed
226

Gael  MILLOT's avatar
Gael MILLOT committed
227
228
2) function fun_dataframe_flipping() has been renamed fun_dataframe_remodeling()

Gael  MILLOT's avatar
Gael MILLOT committed
229
3) more examples added, also draws added in the .docx file for fun_dataframe_remodeling()
Gael  MILLOT's avatar
Gael MILLOT committed
230
231


Gael  MILLOT's avatar
Gael MILLOT committed
232
233
234
235
236
## 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


Gael  MILLOT's avatar
Gael MILLOT committed
237
238
239
240
241
242
243
244
245
246
247
## 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

2) Bug corrected in fun_graph_param_prior_plot() function

3) Bug corrected in fun_refactorization() function


## v1.3

Gael  MILLOT's avatar
Gael MILLOT committed
248
1) fun_1D_comp() function improved: provide the common elements, common names and common levels if exist
Gael  MILLOT's avatar
Gael MILLOT committed
249
250