fun_trim() bug fixed

cute_little_R_functions.R

@@ -34,53 +34,53 @@
 ################ Object analysis    2
 ######## fun_check() #### check class, type, length, etc., of objects   2
-######## fun_secu() #### verif that local variables are not present in other envs   10
-######## fun_info() #### recover object information 12
-######## fun_head() #### head of the left or right of big 2D objects    14
-######## fun_tail() #### tail of the left or right of big 2D objects    15
-######## fun_comp_1d() #### comparison of two 1D datasets (vectors, factors, 1D tables) 16
-######## fun_comp_2d() #### comparison of two 2D datasets (row & col names, dimensions, etc.)   20
-######## fun_comp_list() #### comparison of two lists   26
-######## fun_test() #### test combinations of argument values of a function and return errors (and graphs)  29
-################ Object modification    43
-######## fun_name_change() #### check a vector of character strings and modify any string if present in another vector  43
-######## fun_df_remod() #### remodeling a data frame to have column name as a qualitative values and vice-versa 45
-######## fun_round() #### rounding number if decimal present    47
-######## fun_mat_rotate() #### 90° clockwise matrix rotation    49
-######## fun_mat_num2color() #### convert a numeric matrix into hexadecimal color matrix    50
-######## fun_mat_op() #### assemble several matrices with operation 53
-######## fun_mat_inv() #### return the inverse of a square matrix   56
-######## fun_mat_fill() #### fill the empty half part of a symmetric square matrix  57
-######## fun_permut() #### progressively breaks a vector order  61
-######## fun_slide() #### return a computation made on a vector using a sliding window  71
-################ Graphics management    78
-######## fun_width() #### window width depending on classes to plot 78
-######## fun_open() #### open a GUI or pdf graphic window   80
-######## fun_prior_plot() #### set graph param before plotting (erase axes for instance)    84
-######## fun_scale() #### select nice label numbers when setting number of ticks on an axis 88
-######## fun_inter_ticks() #### define coordinates of secondary ticks   93
-######## fun_post_plot() #### set graph param after plotting (axes redesign for instance)   97
-######## fun_close() #### close specific graphic windows    108
-################ Standard graphics  110
-######## fun_empty_graph() #### text to display for empty graphs    110
-################ gg graphics    112
-######## fun_gg_palette() #### ggplot2 default color palette    112
-######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle  113
-######## fun_gg_get_legend() #### get the legend of ggplot objects  116
-######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer  118
-######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required    121
-######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally)   121
-######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required  122
-######## fun_gg_empty_graph() #### text to display for empty graphs 135
-################ Graphic extraction 137
-######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs 137
-######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation   146
-################ Import 178
-######## fun_pack() #### check if R packages are present and import into the working environment    178
-######## fun_python_pack() #### check if python packages are present    180
-################ Print / Exporting results (text & tables)  182
-######## fun_report() #### print string or data object into output file 182
-######## fun_get_message() #### return error/warning/other messages of an expression (that can be exported) 185
+######## fun_secu() #### verif that local variables are not present in other envs   11
+######## fun_info() #### recover object information 13
+######## fun_head() #### head of the left or right of big 2D objects    15
+######## fun_tail() #### tail of the left or right of big 2D objects    16
+######## fun_comp_1d() #### comparison of two 1D datasets (vectors, factors, 1D tables) 17
+######## fun_comp_2d() #### comparison of two 2D datasets (row & col names, dimensions, etc.)   21
+######## fun_comp_list() #### comparison of two lists   29
+######## fun_test() #### test combinations of argument values of a function and return errors (and graphs)  31
+################ Object modification    46
+######## fun_name_change() #### check a vector of character strings and modify any string if present in another vector  46
+######## fun_df_remod() #### remodeling a data frame to have column name as a qualitative values and vice-versa 47
+######## fun_round() #### rounding number if decimal present    50
+######## fun_mat_rotate() #### 90° clockwise matrix rotation    52
+######## fun_mat_num2color() #### convert a numeric matrix into hexadecimal color matrix    53
+######## fun_mat_op() #### assemble several matrices with operation 56
+######## fun_mat_inv() #### return the inverse of a square matrix   59
+######## fun_mat_fill() #### fill the empty half part of a symmetric square matrix  60
+######## fun_permut() #### progressively breaks a vector order  64
+######## fun_slide() #### return a computation made on a vector using a sliding window  75
+################ Graphics management    83
+######## fun_width() #### window width depending on classes to plot 83
+######## fun_open() #### open a GUI or pdf graphic window   85
+######## fun_prior_plot() #### set graph param before plotting (erase axes for instance)    89
+######## fun_scale() #### select nice label numbers when setting number of ticks on an axis 93
+######## fun_inter_ticks() #### define coordinates of secondary ticks   98
+######## fun_post_plot() #### set graph param after plotting (axes redesign for instance)   102
+######## fun_close() #### close specific graphic windows    114
+################ Standard graphics  116
+######## fun_empty_graph() #### text to display for empty graphs    116
+################ gg graphics    117
+######## fun_gg_palette() #### ggplot2 default color palette    117
+######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle  119
+######## fun_gg_get_legend() #### get the legend of ggplot objects  124
+######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer  126
+######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required    129
+######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally)   129
+######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required  130
+######## fun_gg_empty_graph() #### text to display for empty graphs 143
+################ Graphic extraction 145
+######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs 145
+######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation   154
+################ Import 188
+######## fun_pack() #### check if R packages are present and import into the working environment    188
+######## fun_python_pack() #### check if python packages are present    190
+################ Print / Exporting results (text & tables)  193
+######## fun_report() #### print string or data object into output file 193
+######## fun_get_message() #### return error/warning/other messages of an expression (that can be exported) 196
 ################################ FUNCTIONS ################################
@@ -6058,7 +6058,7 @@ stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"),
 }
 # end argument checking
 # main code
-if(class(data)%in% c("matrix", "array")){
+if(all(class(data)%in% c("matrix", "array"))){
 data <- as.vector(data)
 }
 na.nb <- NULL
@@ -7966,9 +7966,9 @@ return(output) # do not use cat() because the idea is to reuse the message
-# 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
+# check s/lapply everywhere with get: done cute boxplot scatter anova comat
+# get() with env everywhere: done cute boxplot scatter anova comat
+# add the new NA and NULL check cute, done for all the rest
 fun_gg_boxplot <- function(
 data1,