Commit 56cafdb9 authored by Gael's avatar Gael
Browse files

release v10.5.0

parent 7de726b2
......@@ -170,7 +170,12 @@ Gitlab developers
## WHAT'S NEW IN
### v10.3.0
### v10.5.0
1) fun_codon_finder() improved
### v10.4.0
1) fun_codon_finder(): start argument replaced by begin
......
......@@ -122,7 +122,7 @@
######## fun_comp_2d() #### comparison of two 2D datasets (row & col names, dimensions, etc.) 31
######## fun_comp_list() #### comparison of two lists 40
######## fun_test() #### test combinations of argument values of a function and return errors (and graphs) 42
################ Object modification 59
################ Object modification 60
######## fun_name_change() #### check a vector of character strings and modify any string if present in another vector 60
######## fun_df_remod() #### remodeling a data frame to have column name as a qualitative values and vice-versa 61
######## fun_round() #### rounding number if decimal present 64
......@@ -134,34 +134,35 @@
######## fun_permut() #### progressively breaks a vector order 78
######## fun_slide() #### return a computation made on a vector using a sliding window 89
######## fun_codon2aa() #### convert codon to amino acid using standard genetic code 98
################ Graphics management 101
######## fun_width() #### window width depending on classes to plot 101
######## fun_open() #### open a GUI or pdf graphic window 102
######## fun_prior_plot() #### set graph param before plotting (erase axes for instance) 106
######## fun_scale() #### select nice label numbers when setting number of ticks on an axis 111
######## fun_inter_ticks() #### define coordinates of secondary ticks 116
######## fun_post_plot() #### set graph param after plotting (axes redesign for instance) 120
######## fun_close() #### close specific graphic windows 133
################ Standard graphics 134
######## fun_empty_graph() #### text to display for empty graphs 134
################ gg graphics 136
######## fun_gg_palette() #### ggplot2 default color palette 136
######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle 138
######## fun_gg_get_legend() #### get the legend of ggplot objects 142
######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer 145
######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required 148
######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally) 148
######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required 148
######## fun_gg_empty_graph() #### text to display for empty graphs 157
################ Graphic extraction 159
######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs 159
######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation 168
################ Import 204
######## fun_pack() #### check if R packages are present and import into the working environment 204
######## fun_python_pack() #### check if python packages are present 205
################ Print / Exporting results (text & tables) 208
######## fun_report() #### print string or data object into output file 208
######## fun_get_message() #### return error/warning/other messages of an expression (that can be exported) 211
######## fun_codon_finder() #### gives the codon number and position in the codon of nucleotid positions 101
################ Graphics management 104
######## fun_width() #### window width depending on classes to plot 104
######## fun_open() #### open a GUI or pdf graphic window 105
######## fun_prior_plot() #### set graph param before plotting (erase axes for instance) 110
######## fun_scale() #### select nice label numbers when setting number of ticks on an axis 114
######## fun_inter_ticks() #### define coordinates of secondary ticks 119
######## fun_post_plot() #### set graph param after plotting (axes redesign for instance) 123
######## fun_close() #### close specific graphic windows 136
################ Standard graphics 137
######## fun_empty_graph() #### text to display for empty graphs 137
################ gg graphics 139
######## fun_gg_palette() #### ggplot2 default color palette 139
######## fun_gg_just() #### ggplot2 justification of the axis labeling, depending on angle 141
######## fun_gg_get_legend() #### get the legend of ggplot objects 145
######## fun_gg_point_rast() #### ggplot2 raster scatterplot layer 148
######## fun_gg_boxplot() #### ggplot2 boxplot + background dots if required 151
######## fun_gg_scatter() #### ggplot2 scatterplot + lines (up to 6 overlays totally) 151
######## fun_gg_heatmap() #### ggplot2 heatmap + overlaid mask if required 151
######## fun_gg_empty_graph() #### text to display for empty graphs 160
################ Graphic extraction 162
######## fun_trim() #### display values from a quantitative variable and trim according to defined cut-offs 162
######## fun_segmentation() #### segment a dot cloud on a scatterplot and define the dots from another cloud outside the segmentation 171
################ Import 207
######## fun_pack() #### check if R packages are present and import into the working environment 207
######## fun_python_pack() #### check if python packages are present 208
################ Print / Exporting results (text & tables) 211
######## fun_report() #### print string or data object into output file 211
######## fun_get_message() #### return error/warning/other messages of an expression (that can be exported) 214
 
 
################################ FUNCTIONS ################################
......@@ -4420,9 +4421,6 @@ return(output)
######## fun_codon_finder() #### gives the codon number and position in the codon of nucleotid positions
 
 
######## fun_codon_finder() #### gives the codon number and position in the codon of nucleotid positions
fun_codon_finder <- function(
pos,
begin,
......@@ -4438,10 +4436,9 @@ end
# begin: single integer indicating the position of the first base of the coding sequence
# end: single indicating the position of the last base of the coding sequence
# RETURN
# a matrix with row names corresponding to the pos argument input, each row being the result of each values of pos argument
# Column names are
# a data frame with column names:
# pos: values of the pos argument
# codon_nb: the codon number in the CDS encompassing the pos input
# codon_nb: the codon number in the CDS encompassing the pos value
# codon_pos: the position of pos in the codon (either 1, 2 or 3)
# codon_begin: the first base position of the codon
# codon_end: the last base position of the codon
......@@ -4549,27 +4546,25 @@ stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"),
# main code
first <- seq.int(from = begin, to = end, by = 3)
last <- seq.int(from = begin + 2, to = end, by = 3)
tempo <- sapply(X = pos, FUN = function(x = X){
tempo <- lapply(X = pos, FUN = function(x = X){
tempo.log <- x >= first & x <= last
if(sum(tempo.log, na.rm = TRUE) != 1){ # check that 1 possible TRUE
tempo.cat <- paste0("ERROR IN ", function.name, ": INTERNAL ERROR. CODE HAS TO BE MODIFIED")
stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n"), call. = FALSE) # == in stop() to be able to add several messages between ==
}else{
codon_nb <- which(tempo.log)
codon_pos <- (x - (begin + (codon_nb - 1) * 3) + 1)
codon_begin <- first[tempo.log]
codon_end <- last[tempo.log]
codon_pos <- as.integer((x - (begin + (codon_nb - 1) * 3) + 1))
codon_begin <- as.integer(first[tempo.log])
codon_end <- as.integer(last[tempo.log])
}
return(list(codon_nb = codon_nb, codon_pos = codon_pos, codon_begin = codon_begin, codon_end = codon_end))
return(data.frame(codon_nb = codon_nb, codon_pos = codon_pos, codon_begin = codon_begin, codon_end = codon_end))
})
output <- data.frame(pos = pos, t(tempo))
tempo <- do.call("rbind", tempo)
output <- data.frame(pos = as.integer(pos), tempo)
return(output)
}
 
 
################ Graphics management
 
 
......@@ -11312,8 +11307,6 @@ return(output) # this plots the graph if return.ggplot is TRUE and if no assignm
 
 
 
# add density
# rasterise all kind: https://cran.r-project.org/web/packages/ggrastr/vignettes/Raster_geoms.html
# log not good: do not convert as in boxplot
......
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