Commit d33134b5 authored by Gael  MILLOT's avatar Gael MILLOT
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tempo saving

parent 4732d9c9
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......@@ -21,55 +21,55 @@
################################ OUTLINE ################################
 
 
################ Object analysis 2
######## fun_check() #### check class, type, length, etc., of objects 2
######## fun_info() #### recover object information 8
######## fun_1d_comp() #### comparison of two 1D datasets (vectors, factors, 1D tables) 9
######## fun_2d_comp() #### comparison of two 2D datasets (row & col names, dimensions, etc.) 13
######## fun_2d_head() #### head of the left or right of big 2D objects 20
######## fun_2d_tail() #### tail of the left or right of big 2D objects 21
######## fun_list_comp() #### comparison of two lists 22
################ Object modification 24
######## fun_name_change() #### check a vector of character strings and modify any string if present in another vector 24
######## fun_df_remod() #### remodeling a data frame to have column name as a qualitative values and vice-versa 26
######## fun_merge() #### merge the columns of two 2D objects, by common rows 29
######## fun_round() #### rounding number if decimal present 33
######## fun_mat_rotate() #### 90 clockwise matrix rotation 35
######## fun_mat_num2color() #### convert a numeric matrix into hexadecimal color matrix 35
######## fun_mat_op() #### assemble several matrices with operation 38
######## fun_mat_inv() #### return the inverse of a square matrix 41
######## fun_mat_fill() #### fill the empty half part of a symmetric square matrix 42
######## fun_permut() #### progressively breaks a vector order 45
################ Graphics management 55
######## fun_width() #### window width depending on classes to plot 56
######## fun_open() #### open a GUI or pdf graphic window 57
######## fun_prior_plot() #### set graph param before plotting (erase axes for instance) 60
######## fun_scale() #### select nice label numbers when setting number of ticks on an axis 64
######## fun_post_plot() #### set graph param after plotting (axes redesign for instance) 69
######## fun_close() #### close specific graphic windows 80
################ Standard graphics 81
######## fun_empty_graph() #### text to display for empty graphs 82
################ gg graphics 83
######## fun_gg_palette() #### ggplot2 default color palette 83
######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle 84
######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer 87
######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally) 90
######## fun_gg_bar_mean() #### ggplot2 mean barplot + overlaid dots if required 126
######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required 161
######## fun_gg_bar_prop() #### ggplot2 proportion barplot 166
######## fun_gg_strip() #### ggplot2 stripchart + mean/median 166
######## fun_gg_violin() #### ggplot2 violins 166
######## fun_gg_line() #### ggplot2 lines + background dots and error bars 166
######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required 168
######## fun_gg_empty_graph() #### text to display for empty graphs 182
################ Graphic extraction 184
######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs 184
######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation 192
################ Import 224
######## fun_pack() #### check if R packages are present and import into the working environment 224
######## fun_python_pack() #### check if python packages are present 226
################ Exporting results (text & tables) 227
######## fun_report() #### print string or data object into output file 227
################ Object analysis 2
######## fun_check() #### check class, type, length, etc., of objects 2
######## fun_info() #### recover object information 8
######## fun_1d_comp() #### comparison of two 1D datasets (vectors, factors, 1D tables) 9
######## fun_2d_comp() #### comparison of two 2D datasets (row & col names, dimensions, etc.) 13
######## fun_2d_head() #### head of the left or right of big 2D objects 20
######## fun_2d_tail() #### tail of the left or right of big 2D objects 21
######## fun_list_comp() #### comparison of two lists 22
################ Object modification 24
######## fun_name_change() #### check a vector of character strings and modify any string if present in another vector 24
######## fun_df_remod() #### remodeling a data frame to have column name as a qualitative values and vice-versa 26
######## fun_merge() #### merge the columns of two 2D objects, by common rows 29
######## fun_round() #### rounding number if decimal present 33
######## fun_mat_rotate() #### 90 clockwise matrix rotation 35
######## fun_mat_num2color() #### convert a numeric matrix into hexadecimal color matrix 35
######## fun_mat_op() #### assemble several matrices with operation 38
######## fun_mat_inv() #### return the inverse of a square matrix 41
######## fun_mat_fill() #### fill the empty half part of a symmetric square matrix 42
######## fun_permut() #### progressively breaks a vector order 45
################ Graphics management 55
######## fun_width() #### window width depending on classes to plot 56
######## fun_open() #### open a GUI or pdf graphic window 57
######## fun_prior_plot() #### set graph param before plotting (erase axes for instance) 60
######## fun_scale() #### select nice label numbers when setting number of ticks on an axis 64
######## fun_post_plot() #### set graph param after plotting (axes redesign for instance) 69
######## fun_close() #### close specific graphic windows 80
################ Standard graphics 81
######## fun_empty_graph() #### text to display for empty graphs 82
################ gg graphics 83
######## fun_gg_palette() #### ggplot2 default color palette 83
######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle 84
######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer 87
######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally) 90
######## fun_gg_bar_mean() #### ggplot2 mean barplot + overlaid dots if required 126
######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required 161
######## fun_gg_bar_prop() #### ggplot2 proportion barplot 166
######## fun_gg_strip() #### ggplot2 stripchart + mean/median 166
######## fun_gg_violin() #### ggplot2 violins 166
######## fun_gg_line() #### ggplot2 lines + background dots and error bars 166
######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required 168
######## fun_gg_empty_graph() #### text to display for empty graphs 182
################ Graphic extraction 184
######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs 184
######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation 192
################ Import 224
######## fun_pack() #### check if R packages are present and import into the working environment 224
######## fun_python_pack() #### check if python packages are present 226
################ Exporting results (text & tables) 227
######## fun_report() #### print string or data object into output file 227
 
 
################################ FUNCTIONS ################################
......
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