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diff --git a/MarkdownReports.unused.R b/MarkdownReports.unused.R
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-######################################################################
-# Funcitons to Generate Markdown (html) Reports with R
-######################################################################
-
-# "Unused version:"
-# MarkDown_Img_Logger_PDF_and_PNG <- function(fname_wo_ext) { # insert 2 links, one for PDF, one for PNG version of the same image (png files are needed for web or email sharing!!!)
-# splt = strsplit(fname_wo_ext,"/"); fn = splt[[1]][l(splt[[1]])] # Split and select the trailing file name
-# llogit(kollapse ('![', fn, ']', '(', fname_wo_ext,'.pdf)', print=F))
-# llogit(kollapse ('![', fn, ']', '(', fname_wo_ext,'.png)', print=F)) # link to a png file to use locally
-# }
-
-
-# "Unused version:"
-# MarkDown_Img_Logger_4GitHub <- function(fname_wo_ext) { # insert 2 links, one for PDF, one for PNG version of the same image (png files are needed for web or email sharing!!!)
-# splt = strsplit(fname_wo_ext,"/"); fn = splt[[1]][l(splt[[1]])] # Split and select the trailing file name
-# llogit(kollapse ('![', fn, ']', '(Reports/',fn ,'.png)', print=F))
-# }
-
-# "Unused version:"
-# MarkDown_Img_Logger_PDF_and_PNG_GitHub <- function (FullPathtoPDF) {
-# # MarkDown_Img_Logger_PDF_and_PNG_GitHub is a function to put a png and a pdf link to .md log file.
-# print("Link to both pdf and png versions are created in the .md logfile.")
-# trunk = strsplit(FullPathtoPDF, "\\.pdf")[[1]]
-# splt = strsplit(trunk,"/"); fname_wo_ext = splt[[1]][l(splt[[1]])] # Split and select the trailing file name
-# llogit(kollapse ('![]', '(', trunk,'.pdf)', print=F))
-# if (exists("png4Github") & png4Github ==T ) { dirnm = strsplit(OutDir, split = "/")[[1]]; dirnm = dirnm[length(dirnm)]
-# llogit(kollapse ('![]', '(Reports/' ,dirnm,'/', fname_wo_ext,'.png)', print=F)) # link to a png file that needs to be uploaded to GitHub-wiki under Reports/Folder-of-the-report/
-# } else { llogit(kollapse ('![', fname_wo_ext, ']', '(', trunk,'.png)', print=F))} # link to png 4 local use
-# }
-
-
-# MarkDown_Table_writer_DF_RowColNames <- function (df, FnP=Log_PnF, percentify =FALSE, title_of_table = NA) {
-# if (is.na(title_of_table)) { t = substitute(df) } else {t = title_of_table} # Format title of table
-# title_of_table = paste("\n#### ", t)
-# write ( title_of_table, Log_PnF, append=T)
-# h = paste(colnames(df), collapse = " \t| ") # Format header
-# h = paste ("\n| |", h, " |",collapse = "")
-# ncolz = dim(df)[2]+1; nrows = dim(df)[1]
-# rn = rownames (df)
-# sep = kollapse(rep("| ---", ncolz)," |", print=F)
-# if (exists("Log_PnF") ) { write ( h, Log_PnF, append=T); write ( sep, Log_PnF, append=T)
-# for (r in 1:nrows){
-# if (is.numeric(unlist(df[r,]))) { b = iround(df[r,]) # Round Nr-s
-# if(percentify) { b =percentage_formatter(b)} # make %
-# } else { b = df[r,]}
-# b = paste ( unlist(b), collapse = " \t| ") # Format table body
-# # This looked errorous: I needed to transpose it to make it work. Why not as a simple vector?
-# # b = paste ( as.data.frame(b), collapse = " \t| ") # Format table body
-# b = paste ("|", rn[r], "\t|", b, " |",collapse = "")
-# write ( b, Log_PnF, append=T)
-# } # for
-# }
-# else { print("NOT LOGGED: Log path and filename is not defined in Log_PnF") } # if cannot print
-# }
-
-
-# MarkDown_Table_writer_NamedVector <- function (NamedVector, FnP=Log_PnF, percentify =FALSE, title_of_table = NA) {
-# if (is.na(title_of_table)) { t = substitute(NamedVector) } else {t = title_of_table} # Format title of table
-# title_of_table = paste("\n#### ", t)
-# write ( title_of_table, Log_PnF, append=T)
-# if (!is.table(NamedVector)) {if (is.numeric(NamedVector)) {NamedVector = iround(NamedVector)}}
-# h = paste(names(NamedVector), collapse = " \t| ") # Format header
-# h = paste ("\n| ", h, " |",collapse = "")
-# ncolz = l(NamedVector)
-# sep = kollapse(rep("| ---", ncolz)," |", print=F)
-# if (exists("Log_PnF") ) {
-# write ( h, Log_PnF, append=T)
-# write ( sep, Log_PnF, append=T)
-# if(percentify & is.numeric(NamedVector)) { NamedVector =percentage_formatter(NamedVector)} # make %
-# b = paste ( NamedVector, collapse = " \t| ") # Format table body
-# b = paste ("|", b, " |",collapse = "")
-# write ( b, Log_PnF, append=T)
-# } else { print("NOT LOGGED: Log path and filename is not defined in Log_PnF") } # if cannot print
-# }
diff --git a/MarkdownReports/R/MarkdownReports.R.bac b/MarkdownReports/R/MarkdownReports.R.bac
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index c7fbaa5..0000000
--- a/MarkdownReports/R/MarkdownReports.R.bac
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@@ -1,1024 +0,0 @@
-## MarkdownReports.R
-
-
-#' kollapse
-#'
-#' Collapses values and strings to one string (without a white space). It also prints the results (good for a quick check)
-#' @param ... Variables (strings, vectors) to be collapsed in consecutively.
-#' @param print Print the results to the terminal. TRUE by default.
-#' @examples kollapse("Hello ", "you ", 3, ", " , 11, " year old kids.")
-#' @export
-
-kollapse <-function (..., print = T) {
- if (print == T) {
- print(paste0(c(...), collapse = ""))
- }
- paste0(c(...), collapse = "")
-}
-
-
-#' any_print
-#'
-#' A more flexible printing function that collapses any variable passed to it by white spaces.
-#' @param ... Variables (strings, vectors) to be collapsed in consecutively.
-#' @examples any_print ("Hello ", "you ", 3, ", " , 11, " year old kids.")
-#' @export
-
-any_print <-function (...) {
- argument_list <- c(...)
- print(paste(argument_list, collapse = " "))
-}
-
-
-#' iround
-#'
-#' Rounds a value to the significant amount of digits. Its a wrapper for signif().
-#' @param x Unrounded number.
-#' @param digitz Number of digits to keep. 3 by default.
-#' @examples iround (x = , digitz = 3)
-#' @export
-
-iround <-function (x, digitz = 3) {
- signif(x, digits = digitz)
-}
-
-
-#' percentage_formatter
-#'
-#' Parse a string of 0-100% from a number between 0 and 1.
-#' @param x A vector of numbers between [0,1]/
-#' @param digitz Number of digits to keep. 3 by default.
-#' @examples percentage_formatter (x = , digitz = 3)
-#' @export
-
-percentage_formatter <-function (x, digitz = 3) {
- a = paste(100 * iround(x, digitz), "%", sep = " ")
- a[a == "NaN %"] = NaN
- a[a == "NA %"] = NA
- return(a)
-}
-
-
-#' create_set_OutDir
-#'
-#' Create or set the output directory of the script, and set the "OutDir" variable that is used by all ~wplot functions.
-#' @param ... Variables (strings, vectors) to be collapsed in consecutively.
-#' @examples create_set_OutDir (... = )
-#' @export
-
-create_set_OutDir <-function (...) {
- OutDir = kollapse(..., print = F)
- print(OutDir)
- if (!exists(OutDir)) {
- dir.create(OutDir)
- }
- assign("OutDir", OutDir, envir = .GlobalEnv)
-}
-
-
-#' setup_logging_markdown
-#'
-#' Setup the markdown report file, create a sub directory in "OutDir". Its name is stamped with the script name and the modification time. Create the "Log_PnF" variable used by all log-writing and ~wplot functions.
-#' @param fname Name of the report file.
-#' @param title Title of the report.
-#' @param append Set append to TRUE if you do not want to overwrite the previous report. Use continue_logging_markdown() if you return logging into an existing report.
-#' @param png4Github A global variable, defined by this and used by the other functions. If TRUE (default), any link to the .png versions of images will be created in a GitHub compatible format. That means, when you upload your markdown report and the .png images to your GitHub wiki under "Reports/" the links will correctly display the images online.
-#' @examples setup_logging_markdown (fname = , title = , append = T, png4Github = T)
-#' @export
-
-setup_logging_markdown <-function (fname, title = "", append = T, png4Github = T) {
- if (exists("OutDir")) {
- path = OutDir
- }
- else {
- path = getwd()
- any_print("OutDir not defined !!!")
- }
- Log_PnF <- kollapse(path, "/", fname, ".log.md")
- if (nchar(title)) {
- write(paste("# ", title), Log_PnF, append = append)
- }
- else {
- write(paste("# ", fname, "Report"), Log_PnF, append = append)
- }
- write(kollapse(" Modified: ", format(Sys.time(), "%d/%m/%Y | %H:%M | by: "), fname), Log_PnF,
- append = T)
- OutImg = kollapse(OutDir, "/", substr(fname, 1, nchar(fname)), "_", format(Sys.time(), "%Y_%m_%d-%Hh"),
- print = F)
- if (!exists(OutImg)) {
- dir.create(OutImg)
- assign("OutImg", OutImg, envir = .GlobalEnv)
- }
- assign("Log_PnF", Log_PnF, envir = .GlobalEnv)
- assign("png4Github", png4Github, envir = .GlobalEnv)
-}
-
-
-#' continue_logging_markdown
-#'
-#' Continue writing to an existing report file.
-#' @param fname Name of the report file.
-#' @examples continue_logging_markdown (fname = )
-#' @export
-
-continue_logging_markdown <-function (fname) {
- if (exists("OutDir")) {
- path = OutDir
- }
- else {
- path = getwd()
- any_print("OutDir not defined !!!")
- }
- Log_PnF <- kollapse(path, "/", fname, ".log.md", print = F)
- return(Log_PnF)
- OutImg = kollapse(OutDir, "/", substr(fname, 1, (nchar(fname) - 2)), format(Sys.time(), "%Y_%m_%d-%Hh"),
- print = F)
- if (!exists(OutImg)) {
- dir.create(OutImg)
- assign("OutImg", OutImg, envir = .GlobalEnv)
- }
- return(OutImg)
-}
-
-
-#' log_settings_MarkDown
-#'
-#' Log the parameters & settings used in the script in a table format.
-#' @param ... Variables (strings, vectors) to be collapsed in consecutively.
-#' @examples log_settings_MarkDown (... = )
-#' @export
-
-log_settings_MarkDown <-function (...) {
- call <- match.call()
- namez = sapply(as.list(call[-1]), deparse)
- value = c(...)
- value = as.data.frame(value)
- rownames(value) = namez
- MarkDown_Table_writer_DF_RowColNames((value), title_of_table = "Settings")
-}
-
-
-#' llprint
-#'
-#' Collapse by white spaces a sentence from any variable passed on to the function. Print the sentence to the screen and write it to your markdown report file, if the "Log_PnF" variable is defined.
-#' @param ... Variables (strings, vectors) to be collapsed in consecutively.
-#' @examples llprint (... = )
-#' @export
-
-llprint <-function (...) {
- argument_list <- c(...)
- LogEntry = print(paste(argument_list, collapse = " "))
- if (exists("Log_PnF")) {
- write(kollapse("\n", LogEntry, print = F), Log_PnF, append = T)
- }
- else {
- print("NOT LOGGED: Log path and filename is not defined in Log_PnF")
- }
-}
-
-
-#' llogit
-#'
-#' Collapse by white spaces a sentence from any variable passed on to the function. llogit() writes it to your markdown report file, if the "Log_PnF" variable is defined. It does not print the sentence to the screen.
-#' @param ... Variables (strings, vectors) to be collapsed in consecutively.
-#' @examples llogit (... = )
-#' @export
-
-llogit <-function (...) {
- argument_list <- c(...)
- LogEntry = paste(argument_list, collapse = " ")
- LogEntry = gsub("^ +| +$", "", LogEntry)
- if (!exists("Log_PnF")) {
- print("Log path and filename is not defined in Log_PnF")
- }
- write(kollapse("\n", LogEntry, print = F), Log_PnF, append = T)
-}
-
-
-#' MarkDown_ImgLink_formatter
-#'
-#' Format a markdown image reference (link) from the file path to the file. It can parse the file path, if you pass it in separate variables and strings. E.g. MarkDown_ImgLink_formatter(Directory, "MyImage.png").
-#' @param ... Variables (strings, vectors) to be collapsed in consecutively.
-#' @examples MarkDown_ImgLink_formatter (... = )
-#' @export
-
-MarkDown_ImgLink_formatter <-function (...) {
- FullPath = kollapse(..., print = F)
- splt = strsplit(FullPath, "/")
- fn = splt[[1]][l(splt[[1]])]
- kollapse("![", fn, "]", "(", FullPath, ")", print = F)
-}
-
-
-#' MarkDown_Img_Logger_PDF_and_PNG
-#'
-#' Format a markdown image reference (link) to a .pdf and .png versions of graph, and insert both links to the markdown report, set by "Log_PnF". If the "png4Github" variable is set, the .png-link is set up such, that you can upload the whole report with the .png image into your GitHub repo's wiki, under "Reports"/OutDir/ (Reports is a literal string, OutDir is the last/deepest directory name in the "OutDir" variable. See create_set_OutDir() function.). This function is called by the ~wplot functions.
-#' @param fname_wo_ext Name of the image file where markdown links going to point to.
-#' @examples MarkDown_Img_Logger_PDF_and_PNG (fname_wo_ext = )
-#' @export
-
-MarkDown_Img_Logger_PDF_and_PNG <-function (fname_wo_ext) {
- splt = strsplit(fname_wo_ext, "/")
- fn = splt[[1]][l(splt[[1]])]
- llogit(kollapse("![]", "(", fname_wo_ext, ".pdf)", print = F))
- if (exists("png4Github") & png4Github == T) {
- dirnm = strsplit(OutDir, split = "/")[[1]]
- dirnm = dirnm[length(dirnm)]
- llogit(kollapse("![]", "(Reports/", dirnm, "/", fname_wo_ext, ".png)", print = F))
- }
- else {
- llogit(kollapse("![", fn, "]", "(", fname_wo_ext, ".png)", print = F))
- }
-}
-
-
-#' MarkDown_Table_writer_DF_RowColNames
-#'
-#' Take an R data frame with row- and column- names, parse a markdown table from it, and write it to the markdown report, set by "Log_PnF".
-#' @param df Input data frame to be plotted
-#' @param FullPath Full path to the file.
-#' @param percentify Format numbers [0,1] to percentages 1-100%.
-#' @param title_of_table Title above the table (in the markdown report).
-#' @examples MarkDown_Table_writer_DF_RowColNames (df = , FullPath = Log_PnF, percentify = F, title_of_table = NA)
-#' @export
-
-MarkDown_Table_writer_DF_RowColNames <-function (df, FullPath = Log_PnF, percentify = F, title_of_table = NA) {
- if (is.na(title_of_table)) {
- t = substitute(df)
- }
- else {
- t = title_of_table
- }
- title_of_table = paste("\n#### ", t)
- write(title_of_table, Log_PnF, append = T)
- h = paste(colnames(df), collapse = " \t| ")
- h = paste("\n| |", h, " |", collapse = "")
- ncolz = dim(df)[2] + 1
- nrows = dim(df)[1]
- rn = rownames(df)
- sep = kollapse(rep("| ---", ncolz), " |", print = F)
- if (exists("Log_PnF")) {
- write(h, Log_PnF, append = T)
- write(sep, Log_PnF, append = T)
- for (r in 1:nrows) {
- if (is.numeric(unlist(df[r, ]))) {
- b = iround(df[r, ])
- if (percentify) {
- b = percentage_formatter(b)
- }
- }
- else {
- b = df[r, ]
- }
- b = paste(b, collapse = " \t| ")
- b = paste("|", rn[r], "\t|", b, " |", collapse = "")
- write(b, Log_PnF, append = T)
- }
- }
- else {
- print("NOT LOGGED: Log path and filename is not defined in Log_PnF")
- }
-}
-
-
-#' MarkDown_Table_writer_NamedVector
-#'
-#' Take an R vector with names, parse a markdown table from it, and write it to the markdown report, set by "Log_PnF".
-#' @param NamedVector A vector for the table body, with names as table header.
-#' @param FullPath Full path to the file.
-#' @param percentify Format numbers [0,1] to percentages 1-100%.
-#' @param title_of_table Title above the table (in the markdown report).
-#' @examples MarkDown_Table_writer_NamedVector (NamedVector = , FullPath = Log_PnF, percentify = F, title_of_table = NA)
-#' @export
-
-MarkDown_Table_writer_NamedVector <-function (NamedVector, FullPath = Log_PnF, percentify = F, title_of_table = NA) {
- if (is.na(title_of_table)) {
- t = substitute(NamedVector)
- }
- else {
- t = title_of_table
- }
- title_of_table = paste("\n#### ", t)
- write(title_of_table, Log_PnF, append = T)
- if (!is.table(NamedVector)) {
- if (is.numeric(NamedVector)) {
- NamedVector = iround(NamedVector)
- }
- }
- h = paste(names(NamedVector), collapse = " \t| ")
- h = paste("\n| ", h, " |", collapse = "")
- ncolz = l(NamedVector)
- sep = kollapse(rep("| ---", ncolz), " |", print = F)
- if (exists("Log_PnF")) {
- write(h, Log_PnF, append = T)
- write(sep, Log_PnF, append = T)
- if (percentify & is.numeric(NamedVector)) {
- NamedVector = percentage_formatter(NamedVector)
- }
- b = paste(NamedVector, collapse = " \t| ")
- b = paste("|", b, " |", collapse = "")
- write(b, Log_PnF, append = T)
- }
- else {
- print("NOT LOGGED: Log path and filename is not defined in Log_PnF")
- }
-}
-
-
-#' wplot
-#'
-#' Create and save scatter plots as .pdf, in "OutDir". If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions. The .png version is not created, only the link is put in place. You can add 2D error bars around the dots, or add lines (ablines) to your plot, by setting "abline" argument to = F (no line, default), "h" (horizontal, further specified by a = y-offset), "v" (vertical, further specified by a = x-offset), "ab" (line with an angle, further specified by a = offset, b = slope).
-#' @param df Input data frame to be plotted_2columns
-#' @param col Color of the plot.
-#' @param pch Define the symbol for each data point. A number [0-25] or any string between ""-s.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param plotname Title of the plot (main parameter) and also the name of the file.
-#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF".
-#' @param errorbar Draw error bars if TRUE. Pass on the value in parameters "upper" and "lower". Refine the look by "w" and "arrow_lwd".
-#' @param upper Size of the upper error bar.
-#' @param lower Size of the lower error bar. By default, it equals the upper error bar.
-#' @param left Size of the left error bar.
-#' @param right Size of the right error bar. By default, it equals the left error bar.
-#' @param w Width of the saved pdf image, in inches.idth
-#' @param arrow_lwd Line width for the error bar arrow. Line width for the error bar arrow.
-#' @param abline Draw a line on the plot. FALSE by default. Use parameters "a" and "b" to draw horizontal, vertical or inclined lines.
-#' @param a X-offset for vertical lines, Y-offset for horizontal, and inclined lines.
-#' @param b Slope of an inclined line.
-#' @param lty Linetype, defined by numbers 1-6.
-#' @param lwd Line width. Set to 2 by default.
-#' @param lcol Color of the line.
-#' @examples wplot (df_2columns = , col = 1, pch = 18, ... = , w = 7, h = 7, plotname = substitute(df_2columns), mdlink = F, errorbar = F, upper = 0, lower = upper, left = 0, right = left, width = 0.1, arrow_lwd = 1, abline = F, a = F, b = F, lty = 1, lwd = 1, lcol = 1)
-#' @export
-
-wplot <-function (df_2columns, col = 1, pch = 18, ..., w = 7, h = 7, plotname = substitute(df_2columns), mdlink = F, errorbar = F, upper = 0, lower = upper, left = 0, right = left, width = 0.1, arrow_lwd = 1,
- abline = F, a = F, b = F, lty = 1, lwd = 1, lcol = 1)
-{
- x = df_2columns[, 1]
- y = df_2columns[, 2]
- fname = kollapse(plotname, ".plot")
- if (errorbar) {
- ylim = range(c(0, (y + upper + abs(0.1 * y)), (y - lower - abs(0.1 * y))))
- xlim = range(c(0, (x + right + abs(0.1 * x)), (1.1 * x - left - abs(0.1 * x))))
- }
- else {
- ylim = range(y)
- xlim = range(x)
- }
- plot(df_2columns, ..., main = plotname, col = col, pch = pch, ylim = ylim, xlim = xlim)
- if (errorbar) {
- arrows(x0 = x, y0 = y + upper, x1 = x, y1 = y - lower, angle = 90, code = 3, length = width,
- lwd = arrow_lwd)
- arrows(x0 = x + left, y0 = y, x1 = x - right, y1 = y, angle = 90, code = 3, length = width, lwd = arrow_lwd)
- }
- if (abline == "h") {
- abline(h = a, lty = lty, lwd = lwd, col = lcol)
- }
- if (abline == "v") {
- abline(v = a, lty = lty, lwd = lwd, col = lcol)
- }
- if (abline == "ab") {
- abline(a = a, b = b, lty = lty, lwd = lwd, col = lcol)
- }
- assign("plotnameLastPlot", fname, envir = .GlobalEnv)
- dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h)
- if (mdlink) {
- MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname)
- }
-}
-
-
-#' wplot_save_this
-#'
-#' Save the currently active graphic device (for complicated plots). Insert links to your markdown report, set by "Log_PnF". Name the file by naming the variable!
-#' @param plotname Title of the plot (main parameter) and also the name of the file.
-#' @param col Color of the plot.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF".
-#' @param ManualName Define the plot's file name manually.
-#' @examples wplot_save_this (plotname = date(), col = gold1, ... = , w = 7, h = 7, mdlink = FALSE, ManualName = FALSE)
-#' @export
-
-wplot_save_this <-function (plotname = date(), col = "gold1", ..., w = 7, h = 7, mdlink = FALSE, ManualName = FALSE) {
- if (plotname == plotnameLastPlot) {
- ManualName = T
- }
- fname = kollapse(plotname, ".plot")
- if (ManualName) {
- fname = plotname
- }
- dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h)
- if (mdlink) {
- MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname)
- }
-}
-
-
-#' whist
-#'
-#' Create and save histograms as .pdf, in "OutDir". If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions. Name the file by naming the variable! Cannot be used with dynamically called variables [e.g. call vectors within a loop]. "filtercol" assumes >= coloring!
-#' @param variable The variable to plot.
-#' @param col Color of the plot.
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param plotname The name of the file.
-#' @param breaks Number of bins.
-#' @param main Title of the plot.
-#' @param xlb X-axis label.
-#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF".
-#' @param h Height of the saved pdf image, in inches.line
-#' @param vline Draw a vertical line at the value you pass on to it. Useful to display a threshold. Design the line by "lty", "lwd" & "lcol" parameters.
-#' @param lty Linetype, defined by numbers 1-6.
-#' @param lwd Line width. Set to 2 by default.
-#' @param lcol Color of the line.
-#' @param filtercol Color bars below / above the threshold with red / green. Define the direction by -1 or 1. Takes effect if "vline" is defined.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @examples whist (variable = , col = gold1, w = 7, h = 7, plotname = substitute(variable), breaks = 20, main = kollapse("Histogram of ", substitute(variable)), xlb = substitute(variable), mdlink = FALSE, hline = F, vline = F, lty = 2, lwd = 3, lcol = 2, filtercol = 0, ... = )
-#' @export
-
-whist <-function (variable, col = "gold1", w = 7, h = 7, plotname = substitute(variable), breaks = 20, main = kollapse("Histogram of ", substitute(variable)), xlb = substitute(variable), mdlink = FALSE, hline = F,
- vline = F, lty = 2, lwd = 3, lcol = 2, filtercol = 0, ...)
-{
- xtra = list(...)
- if (length(variable) > 0) {
- fname = kollapse(plotname, ".hist")
- if (!is.numeric(variable)) {
- variable = table(variable)
- cexNsize = 0.7/abs(log10(length(variable)))
- cexNsize = min(cexNsize, 1)
- barplot(variable, ..., main = main, xlab = xlb, col = col, las = 2, cex.names = cexNsize,
- sub = paste("mean:", iround(mean(variable, na.rm = T)), "CV:", percentage_formatter(cv(variable))))
- }
- else {
- histdata = hist(variable, breaks = breaks, plot = F)
- if (filtercol == 1) {
- col = (histdata$breaks >= vline) + 2
- }
- else if (filtercol == -1) {
- col = (histdata$breaks < vline) + 2
- }
- hist(variable, ..., main = main, breaks = breaks, xlab = xlb, col = col, las = 2)
- }
- if (hline) {
- abline(h = hline, lty = lty, lwd = lwd, col = lcol)
- }
- if (vline & !l(xtra$xlim)) {
- PozOfvline = mean(histdata$mids[c(max(which(histdata$breaks < vline)), min(which(histdata$breaks >=
- vline)))])
- abline(v = PozOfvline, lty = lty, lwd = lwd, col = 1)
- }
- else if (vline & l(xtra$xlim)) {
- abline(v = vline, lty = lty, lwd = lwd, col = 1)
- }
- dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h)
- }
- else {
- any_print(variable, " IS EMPTY")
- }
- assign("plotnameLastPlot", fname, envir = .GlobalEnv)
- if (mdlink) {
- MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname)
- }
-}
-
-
-#' wbarplot
-#'
-#' Create and save bar plots as .pdf, in "OutDir". If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions.
-#' @param variable The variable to plot.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @param col Color of the plot.
-#' @param sub Subtitle for the plot.
-#' @param plotname The name of the file saved.
-#' @param main The title of the plot.
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot.
-#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF".
-#' @param tilted_text Use 45 degree x-labels if TRUE. Useful for long, but not too many labels.
-#' @param hline Draw a horizontal line at the value you pass on to it. Useful to display a threshold. Design the line by "lty", "lwd" & "lcol" parameters.
-#' @param vline Draw a vertical line at the value you pass on to it. Useful to display a threshold. Design the line by "lty", "lwd" & "lcol" parameters.
-#' @param filtercol Color bars below / above the threshold with red / green. Define the direction by -1 or 1. Takes effect if "hline" is defined.
-#' @param lty Linetype, defined by numbers 1-6.
-#' @param lwd Line width. Set to 2 by default.
-#' @param lcol Color of the line.
-#' @param errorbar Draw error bars if TRUE. Pass on the value in parameters "upper" and "lower". Refine the look by "w" and "arrow_lwd".
-#' @param upper Size of the upper error bar.
-#' @param lower Size of the lower error bar. By default, it equals the upper error bar.
-#' @param w Width of the saved pdf image, in inches.idth
-#' @param arrow_lwd Line width for the error bar arrow.
-#' @examples wbarplot (variable = , ... = , col = gold1, sub = F, plotname = substitute(variable), main = substitute(variable), w = 7, h = 7, incrBottMarginBy = 0, mdlink = F, tilted_text = F, hline = F, vline = F, filtercol = 1, lty = 1, lwd = 2, lcol = 2, errorbar = F, upper = 0, lower = upper, width = 0.1, arrow_lwd = 1)
-#' @export
-
-wbarplot <-function (variable, ..., col = "gold1", sub = F, plotname = substitute(variable), main = substitute(variable), w = 7, h = 7, incrBottMarginBy = 0, mdlink = F, tilted_text = F, hline = F, vline = F, filtercol = 1,
- lty = 1, lwd = 2, lcol = 2, errorbar = F, upper = 0, lower = upper, width = 0.1, arrow_lwd = 1)
-{
- fname = kollapse(plotname, ".barplot")
- .ParMarDefault <- par("mar")
- par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4]))
- cexNsize = 0.8/abs(log10(length(variable)))
- cexNsize = min(cexNsize, 1)
- if (sub == T) {
- subtitle = paste("mean:", iround(mean(variable, na.rm = T)), "CV:", percentage_formatter(cv(variable)))
- }
- else if (sub == F) {
- subtitle = ""
- }
- else {
- subtitle = sub
- }
- if (hline & filtercol == 1) {
- col = (variable >= hline) + 2
- }
- if (hline & filtercol == -1) {
- col = (variable < hline) + 2
- }
- if (errorbar) {
- ylim = range(c(0, (variable + upper + abs(0.1 * variable)), variable - lower - abs(0.1 * variable)),
- na.rm = T)
- }
- else {
- ylim = range(0, variable)
- }
- if (tilted_text) {
- xlb = NA
- }
- else {
- xlb = names(variable)
- }
- x = barplot(variable, ..., names.arg = xlb, main = main, sub = subtitle, col = col, las = 2, cex.names = cexNsize,
- ylim = ylim)
- if (hline) {
- abline(h = hline, lty = lty, lwd = lwd, col = lcol)
- }
- if (vline) {
- abline(v = vline, lty = lty, lwd = lwd, col = lcol)
- }
- if (errorbar) {
- arrows(x, variable + upper, x, variable - lower, angle = 90, code = 3, length = width, lwd = arrow_lwd,
- ...)
- }
- if (tilted_text) {
- text(x = x - 0.25, y = -max(nchar(names(variable)))/5, labels = names(variable), xpd = TRUE,
- srt = 45, cex = cexNsize)
- }
- dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h)
- par(mar = .ParMarDefault)
- assign("plotnameLastPlot", fname, envir = .GlobalEnv)
- if (mdlink) {
- MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname)
- }
-}
-
-
-#' wboxplot
-#'
-#' Create and save box plots as .pdf, in "OutDir". If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions.
-#' @param variable The variable to plot.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @param col Color of the plot.
-#' @param plotname Title of the plot (main parameter) and also the name of the file.
-#' @param sub Subtitle for the plot.
-#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot.
-#' @param tilted_text Use 45 degree x-labels if TRUE. Useful for long, but not too many labels.
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF".
-#' @examples wboxplot (variable = , ... = , col = gold1, plotname = as.character(substitute(variable)), sub = FALSE, incrBottMarginBy = 0, tilted_text = F, w = 7, h = 7, mdlink = F)
-#' @export
-
-wboxplot <-function (variable, ..., col = "gold1", plotname = as.character(substitute(variable)), sub = FALSE, incrBottMarginBy = 0, tilted_text = F, w = 7, h = 7, mdlink = F)
-{
- fname = kollapse(plotname, ".boxplot")
- .ParMarDefault <- par("mar")
- par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4]))
- if (tilted_text) {
- xlb = NA
- }
- else {
- xlb = names(variable)
- }
- boxplot(variable, ..., names = xlb, main = plotname, col = col, las = 2)
- if (tilted_text) {
- text(x = 1:l(variable), y = -max(nchar(names(variable)))/2, labels = names(variable), xpd = TRUE,
- srt = 45)
- }
- dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h)
- assign("plotnameLastPlot", fname, envir = .GlobalEnv)
- par(mar = .ParMarDefault)
- if (mdlink) {
- MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname)
- }
-}
-
-
-#' wpie
-#'
-#' Create and save pie charts as .pdf, in "OutDir". If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions.
-#' @param variable The variable to plot.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @param percentage Display percentage instead of counts. TRUE by default.
-#' @param plotname Title of the plot (main parameter) and also the name of the file.
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF".
-#' @examples wpie (variable = , ... = , percentage = TRUE, plotname = substitute(variable), w = 7, h = 7, mdlink = F)
-#' @export
-
-wpie <-function (variable, ..., percentage = TRUE, plotname = substitute(variable), w = 7, h = 7, mdlink = F) {
- fname = kollapse(plotname, ".pie")
- subt = kollapse("Total = ", sum(variable), print = F)
- if (percentage) {
- labs <- paste("(", names(variable), ")", "\n", percentage_formatter(variable/sum(variable)),
- sep = "")
- }
- else {
- labs <- paste("(", names(variable), ")", "\n", variable, sep = "")
- }
- pie(variable, ..., main = plotname, sub = subt, clockwise = T, labels = labs, col = rainbow(l(variable)))
- dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h)
- if (mdlink) {
- MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname)
- }
-}
-
-
-#' wstripchart
-#'
-#' Create and save strip charts as .pdf, in "OutDir". If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions.
-#' @param yalist Input list to be plotted.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @param plotname Title of the plot (main parameter) and also the name of the file.
-#' @param sub Subtitle for the plot.
-#' @param border An optional vector of colors for the outlines of the boxplots. The values in border are recycled if the length of border is less than the number of plots.
-#' @param BoxPlotWithMean Display the mean instead of the median in a boxplot. This is non-standard use of a boxplot, report it.
-#' @param pch Define the symbol for each data point. A number [0-25] or any string between ""-s.
-#' @param pchlwd Define the outline width of the symbol for each data point.
-#' @param pchcex Define the size of the symbol for each data point.
-#' @param bg Background color.
-#' @param col Color of the plot.
-#' @param metod Method for displaying data points to avoid overlap; either"jitter" or "stack". See stripchart().
-#' @param jitter The amount of horizontal scatter added to the individual data points (to avoid overlaps).
-#' @param col Color of the plot.orbyColumn
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot.
-#' @param tilted_text Use 45 degree x-labels if TRUE. Useful for long, but not too many labels.
-#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF".
-#' @examples wstripchart (yalist = , ... = , plotname = as.character(substitute(yalist)), sub = FALSE, border = 1, BoxPlotWithMean = F, pch = 23, pchlwd = 1, pchcex = 1.5, bg = chartreuse2, col = black, metod = jitter, jitter = 0.2, colorbyColumn = F, w = 7, h = 7, incrBottMarginBy = 0, tilted_text = F, mdlink = F)
-#' @export
-
-wstripchart <-function (yalist, ..., plotname = as.character(substitute(yalist)), sub = FALSE, border = 1, BoxPlotWithMean = F, pch = 23, pchlwd = 1, pchcex = 1.5, bg = "chartreuse2", col = "black", metod = "jitter", jitter = 0.2,
- colorbyColumn = F, w = 7, h = 7, incrBottMarginBy = 0, tilted_text = F, mdlink = F)
-{
- .ParMarDefault <- par("mar")
- par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4]))
- cexNsize = 1/abs(log10(length(yalist)))
- cexNsize = min(cexNsize, 1)
- fname = kollapse(plotname, ".stripchart")
- a = boxplot(yalist, plot = F)
- if (colorbyColumn) {
- pchlwd = 5
- pchcex = 0.5
- }
- if (BoxPlotWithMean) {
- a$stats[3, ] = unlist(lapply(yalist, mean))
- }
- if (tilted_text) {
- xlb = F
- }
- else {
- xlb = T
- }
- bxp(a, xlab = "", show.names = xlb, ..., main = plotname, border = border, outpch = NA, las = 2,
- outline = T, cex.axis = cexNsize)
- stripchart(yalist, vertical = TRUE, add = TRUE, method = metod, jitter = jitter, pch = pch, bg = bg,
- col = col, lwd = pchlwd, cex = pchcex)
- if (tilted_text) {
- text(x = 1:l(yalist), y = -max(nchar(names(yalist)))/2, labels = names(yalist), xpd = TRUE, srt = 45)
- }
- dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h)
- par(mar = .ParMarDefault)
- assign("plotnameLastPlot", fname, envir = .GlobalEnv)
- if (mdlink) {
- MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname)
- }
-}
-
-
-#' wstripchart_list
-#'
-#' Create and save stripcharts from a list as .pdf, in "OutDir". This version allows individual coloring of each data point, by a color-list of the same dimension. If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions.
-#' @param yalist Input list to be plotted.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @param plotname Title of the plot (main parameter) and also the name of the file.
-#' @param sub Subtitle for the plot.
-#' @param ylb Y-axis label.
-#' @param xlb X-axis label.
-#' @param border An optional vector of colors for the outlines of the boxplots. The values in border are recycled if the length of border is less than the number of plots.
-#' @param bxpcol Color of the boxplot outlines.
-#' @param pch Define the symbol for each data point. A number [0-25] or any string between ""-s.
-#' @param pchlwd Define the outline width of the symbol for each data point.
-#' @param pchcex Define the size of the symbol for each data point.
-#' @param bg Background color.
-#' @param col Color of the plot.l
-#' @param metod Method for displaying data points to avoid overlap; either"jitter" or "stack". See stripchart().
-#' @param jitter The amount of horizontal scatter added to the individual data points (to avoid overlaps).
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot.
-#' @param tilted_text Use 45 degree x-labels if TRUE. Useful for long, but not too many labels.
-#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF".
-#' @examples wstripchart_list (yalist = , ... = , plotname = as.character(substitute(yalist)), sub = FALSE, ylb = NULL, xlab = NULL, border = 1, bxpcol = 0, pch = 23, pchlwd = 1, pchcex = 1.5, bg = chartreuse2, coll = black, metod = jitter, jitter = 0.2, w = 7, h = 7, incrBottMarginBy = 0, tilted_text = F, mdlink = F)
-#' @export
-
-wstripchart_list <-function (yalist, ..., plotname = as.character(substitute(yalist)), sub = FALSE, ylb = "NULL", xlab = "NULL", border = 1, bxpcol = 0, pch = 23, pchlwd = 1, pchcex = 1.5, bg = "chartreuse2", coll = "black", metod = "jitter",
- jitter = 0.2, w = 7, h = 7, incrBottMarginBy = 0, tilted_text = F, mdlink = F)
-{
- fname = kollapse(plotname, ".stripchart")
- .ParMarDefault <- par("mar")
- par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4]))
- cexNsize = 1/abs(log10(length(list)))
- cexNsize = min(cexNsize, 1)
- if (tilted_text) {
- xlb = F
- }
- else {
- xlb = T
- }
- boxplot(yalist, ..., show.names = xlb, main = plotname, border = border, outline = FALSE, las = 2,
- col = bxpcol, cex.axis = cexNsize)
- for (i in 1:length(yalist)) {
- j = k = i
- if (length(coll) < length(yalist)) {
- j = 1
- }
- if (length(bg) < length(yalist)) {
- k = 1
- }
- stripchart(na.omit(yalist[[i]]), at = i, add = T, vertical = T, method = metod, jitter = jitter,
- pch = pch, bg = bg[[k]], col = coll[[j]], lwd = pchlwd, cex = pchcex)
- }
- if (tilted_text) {
- text(x = 1:l(yalist), y = -max(nchar(names(yalist)))/2, labels = names(yalist), xpd = TRUE, srt = 45)
- }
- dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h)
- par(mar = .ParMarDefault)
- assign("plotnameLastPlot", fname, envir = .GlobalEnv)
- if (mdlink) {
- MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname)
- }
-}
-
-
-#' wvioplot_list
-#'
-#' Create and save violin plots as .pdf, in "OutDir". It requires (and calls) "vioplot" package. If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions.
-#' @param yalist Input list to be plotted.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @param xlb X-axis label.
-#' @param ylb Y-axis label.
-#' @param col Color of the plot.l
-#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot.
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param plotname Title of the plot (main parameter) and also the name of the file.
-#' @param tilted_text Use 45 degree x-labels if TRUE. Useful for long, but not too many labels.
-#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF".
-#' @examples wvioplot_list (yalist = , ... = , xlb = names(yalist), ylb = , coll = c(1:length(yalist)), incrBottMarginBy = 0, w = 7, h = 7, plotname = as.character(substitute(yalist)), tilted_text = F, mdlink = F)
-#' @export
-
-wvioplot_list <-function (yalist, ..., xlb = names(yalist), ylb = "", coll = c(1:length(yalist)), incrBottMarginBy = 0, w = 7, h = 7, plotname = as.character(substitute(yalist)), tilted_text = F, mdlink = F)
-{
- require(vioplot)
- .ParMarDefault <- par("mar")
- par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4]))
- l_list = length(yalist)
- fname = kollapse(plotname, ".vioplot")
- if (length(coll) < l_list) {
- coll = rep(coll, l_list)
- }
- if (tilted_text) {
- xlb = NA
- }
- else {
- xlb = names(yalist)
- }
- plot(0, 0, type = "n", xlim = c(0.5, (l_list + 0.5)), ylim = range(unlist(yalist)), xaxt = "n", xlab = "",
- ylab = ylb, main = plotname)
- for (i in 1:l_list) {
- vioplot(na.omit(yalist[[i]]), ..., at = i, add = T, col = coll[i])
- }
- axis(side = 1, at = 1:l_list, labels = xlb, las = 2)
- if (tilted_text) {
- text(x = 1:l(yalist), y = -max(nchar(names(yalist)))/2, labels = names(yalist), xpd = TRUE, srt = 45)
- }
- dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h)
- par(mar = .ParMarDefault)
- assign("plotnameLastPlot", fname, envir = .GlobalEnv)
- if (mdlink) {
- MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname)
- }
-}
-
-
-#' wviostripchart_list
-#'
-#' Create and save violin plots as .pdf, in "OutDir". It requires (and calls) "vioplot" package. If mdlink =T, it inserts a .pdf and a .png link in the markdown report, set by "Log_PnF". The .png version is not created, only the link is put in place, not to overwrite previous versions.
-#' @param yalist Input list to be plotted.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @param pch Define the symbol for each data point. A number [0-25] or any string between ""-s.
-#' @param viocoll Background color of each individual violing plot.
-#' @param vioborder Border color of each individual violing plot.
-#' @param ylb Y-axis label.
-#' @param plotname Title of the plot (main parameter) and also the name of the file.
-#' @param sub Subtitle for the plot.
-#' @param bg Background color.
-#' @param col Color of the plot.l
-#' @param metod Method for displaying data points to avoid overlap; either"jitter" or "stack". See stripchart().
-#' @param jitter The amount of horizontal scatter added to the individual data points (to avoid overlaps).
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param incrBottMarginBy Increase the blank space at the bottom of the plot. Use if labels do not fit on the plot.
-#' @param mdlink Insert a .pdf and a .png image link in the markdown report, set by "Log_PnF".
-#' @examples wviostripchart_list (yalist = , ... = , pch = 23, viocoll = 0, vioborder = 1, ylb = , plotname = as.character(substitute(yalist)), sub = F, bg = 0, coll = black, metod = jitter, jitter = 0.1, w = 7, h = 7, incrBottMarginBy = 0, mdlink = F)
-#' @export
-
-wviostripchart_list <-function (yalist, ..., pch = 23, viocoll = 0, vioborder = 1, ylb = "", plotname = as.character(substitute(yalist)), sub = F, bg = 0, coll = "black", metod = "jitter", jitter = 0.1, w = 7, h = 7, incrBottMarginBy = 0,
- mdlink = F)
-{
- fname = kollapse(plotname, ".VioStripchart")
- require(vioplot)
- .ParMarDefault <- par("mar")
- par(mar = c(par("mar")[1] + incrBottMarginBy, par("mar")[2:4]))
- l_list = length(yalist)
- plot(0, 0, type = "n", xlim = c(0.5, (l_list + 0.5)), ylim = range(unlist(yalist)), xaxt = "n", xlab = "",
- ylab = ylb, main = plotname)
- for (i in 1:l_list) {
- vioplot(na.omit(yalist[[i]]), ..., at = i, add = T, col = viocoll[i], border = vioborder[i])
- }
- for (i in 1:length(yalist)) {
- j = k = i
- if (length(coll) < length(yalist)) {
- j = 1
- }
- if (length(bg) < length(yalist)) {
- k = 1
- }
- stripchart(na.omit(yalist[[i]]), at = i, add = T, vertical = T, method = metod, jitter = jitter,
- pch = pch, bg = bg[[k]], col = coll[[j]])
- }
- dev.copy2pdf(file = FnP_parser(fname, "pdf"), width = w, height = h)
- par(mar = .ParMarDefault)
- assign("plotnameLastPlot", fname, envir = .GlobalEnv)
- if (mdlink) {
- MarkDown_Img_Logger_PDF_and_PNG(fname_wo_ext = fname)
- }
-}
-
-
-#' whist_dfCol
-#'
-#' Use this version of whist() if you iterate over columns or rows of a data frame. You can name the file by naming the variable. Cannot be used with dynamically called variables [e.g. call vectors within a loop]
-#' @param df Input data frame to be plotted
-#' @param col Color of the plot.Name
-#' @param col Color of the plot.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @examples whist_dfCol (df = , colName = , col = gold, ... = , w = 7, h = 7)
-#' @export
-
-whist_dfCol <-function (df, colName, col = "gold", ..., w = 7, h = 7) {
- stopifnot(colName %in% colnames(df))
- variable = unlist(df[, colName])
- stopifnot(length(variable) > 1)
- plotname = paste(substitute(df), "__", colName, sep = "")
- FullPath = FnP_parser(plotname, "hist.pdf")
- if (!is.numeric(variable)) {
- variable = table(variable)
- cexNsize = 0.7/abs(log10(length(variable)))
- cexNsize = min(cexNsize, 1)
- barplot(variable, ..., main = plotname, col = col, las = 2, cex.names = cexNsize, sub = paste("mean:",
- iround(mean(variable, na.rm = T)), "CV:", percentage_formatter(cv(variable))))
- }
- else {
- zz = hist(variable, ..., plot = F)
- hist(variable, ..., main = plotname, col = col, las = 2, sub = paste("mean:", iround(mean(zz$counts)),
- "median:", iround(median(zz$counts))))
- }
- dev.copy2pdf(file = FullPath, width = w, height = h)
-}
-
-
-#' wbarplot_dfCol
-#'
-#' wbarplot for a column of a data frame.
-#' @param df Input data frame to be plotted
-#' @param col Color of the plot.Name
-#' @param col Color of the plot.
-#' @param w Width of the saved pdf image, in inches.
-#' @param h Height of the saved pdf image, in inches.
-#' @param ... Pass any other parameter of the corresponding plotting function (most of them should work).
-#' @examples wbarplot_dfCol (df = , colName = , col = gold1, w = 7, h = 7, ... = )
-#' @export
-
-wbarplot_dfCol <-function (df, colName, col = "gold1", w = 7, h = 7, ...) {
- stopifnot(colName %in% colnames(df))
- variable = unlist(df[, colName])
- stopifnot(length(variable) > 1)
- plotname = paste(substitute(df), "__", colName, sep = "")
- FullPath = FnP_parser(plotname, "barplot.pdf")
- cexNsize = 0.7/abs(log10(length(variable)))
- cexNsize = min(cexNsize, 1)
- barplot(variable, ..., main = plotname, col = col, las = 2, cex.names = cexNsize, sub = paste("mean:",
- iround(mean(variable, na.rm = T)), "CV:", percentage_formatter(cv(variable))))
- dev.copy2pdf(file = FullPath, width = w, height = h)
-}
-
-
-#' val2col
-#'
-#' This function converts a vector of values("yourdata") to a vector of color levels. One must define the number of colors. The limits of the color scale("zlim") or the break points for the color changes("breaks") can also be defined. when breaks and zlim are defined, breaks overrides zlim. Source: http://menugget.blogspot.nl/2011/09/converting-values-to-color-levels.html
-#' @param yourdata The data, to what the colors will be scaled to.
-#' @param zlim Limits.
-#' @param col Color of the plot.
-#' @param breaks Number of bins.
-#' @examples val2col (yourdata = , zlim = , col = rev(heat.colors(12)), breaks = )
-#' @export
-
-val2col <-function (yourdata, zlim, col = rev(heat.colors(12)), breaks) {
- if (!missing(breaks)) {
- if (length(breaks) != (length(col) + 1)) {
- stop("must have one more break than color")
- }
- }
- if (missing(breaks) & !missing(zlim)) {
- breaks <- seq(zlim[1], zlim[2], length.out = (length(col) + 1))
- }
- if (missing(breaks) & missing(zlim)) {
- zlim <- range(yourdata, na.rm = TRUE)
- zlim[2] <- zlim[2] + c(zlim[2] - zlim[1]) * (0.001)
- zlim[1] <- zlim[1] - c(zlim[2] - zlim[1]) * (0.001)
- breaks <- seq(zlim[1], zlim[2], length.out = (length(col) + 1))
- }
- colorlevels <- col[((as.vector(yourdata) - breaks[1])/(range(breaks)[2] - range(breaks)[1])) * (length(breaks) -
- 1) + 1]
- colorlevels
-}
-
-
-#' error.bar
-#'
-#' Put error bars on top of your bar plots. This functionality is now integrated into MarkdownReporter's wbarplot() function
-#' @param x X-position on the plot.
-#' @param y Y-position on the plot.
-#' @param upper Size of the upper error bar.
-#' @param lower Size of the lower error bar. By default, it equals the upper error bar.
-#' @param width Width of the erro bar whisker.
-#' @param ... Pass any other parameter of the corresponding arrows function (most of them should work).
-#' @examples error.bar (x = , y = , upper = , lower = upper, width = 0.1, ... = )
-#' @export
-
-error.bar <-function (x, y, upper, lower = upper, width = 0.1, ...) {
- stopifnot(length(x) == length(y) & length(y) == length(lower) & length(lower) == length(upper))
- if (l(dim(y)) > 1) {
- arrows(as.vector(x), as.vector(y + upper), as.vector(x), as.vector(y - lower), angle = 90, code = 3,
- length = width , ...)
- }
- else {
- arrows(x, y + upper, x, y - lower, angle = 90, code = 3, length = width , ...)
- }
-}
-
-
-#' barplot.label
-#'
-#' Add extra labels to your bar plots at the top or the base.
-#' @param x X-position of the label.
-#' @param y Y-position of the label.
-#' @param labels Label text.
-#' @param bottom Put labels at the bottom of the bars.
-#' @param relpos_top Relative offset.
-#' @param relpos_bottom Relative offset.
-#' @param ... Pass any other parameter of the corresponding text function (most of them should work).
-#' @examples barplot.label (x = , y = , labels = , bottom = F, relpos_top = 0.9, relpos_bottom = 0.1, ... = )
-#' @export
-
-barplot.label <-function (x, y, labels, bottom = F, relpos_top = 0.9, relpos_bottom = 0.1, ...) {
- stopifnot(length(x) == length(y))
- if (bottom) {
- y = rep(relpos_bottom * max(y, na.rm = T), length(x))
- }
- if (l(dim(x)) > 1) {
- text(as.vector(x), as.vector(y * relpos_top), labels = as.vector(labels), ...)
- }
- else if (l(dim(x)) == 1) {
- text((x), (y), labels = (labels), ...)
- }
-}
-
-
diff --git a/MarkdownReports/R/MarkdownReports.R.bac.gz b/MarkdownReports/R/MarkdownReports.R.bac.gz
new file mode 100644
index 0000000..297464b
Binary files /dev/null and b/MarkdownReports/R/MarkdownReports.R.bac.gz differ
diff --git a/Supplementary/Lecture.md b/Supplementary/Lecture.md
deleted file mode 100644
index baa03a3..0000000
--- a/Supplementary/Lecture.md
+++ /dev/null
@@ -1,42 +0,0 @@
-# Why did I start
-
-- Recommendation
-- My methods did not work that well (very redundant)
-- Cloud copy without me syncing it
-
-# Concept
-
-layers image
-
-add
-push
-commit
-
-
-version control = safety backup + change log
-
-### FAQ
-
-- Private / public
-
-
-## What I got as extra
-
-- Issues as a ToDo list
- - talk with someone
- - linked to the code
- - even on meetings (show it!)
-
-# How to use
-
-- I learnt the git commands, but switched quickly to:
-
-## Demo
-
-### GUI
-
-### Terminal
-
-
-
-Write to the ppl to bring!
\ No newline at end of file
diff --git a/Supplementary/Site.md b/Supplementary/Site.md
deleted file mode 100644
index cf19173..0000000
--- a/Supplementary/Site.md
+++ /dev/null
@@ -1,40 +0,0 @@
-## What is MarkDownLogs
-
-MarkDownLogs is a set of **R** functions that allows you to generate summaries what you discovered with your source code. It helps you to:
-
-1. Write down your findings in an easy, clear and nicely formatted way.
-- Support your findings with quick & pretty figures saved along your report
-- Link and show these in your markdown or html document
-- Share your findings
-
-
-## Why did I make it, why you might like it?
-
-I do exploratory data analysis as daily routine, and I have constant interaction with all sorts of people: supervisors, collaborators, colleagues, etc. I often ...
-
-1. ...have to write emails summarizing the results (text accompanied by figures) of the last few days.
-2. ...find back results a couple of month back, with all tiny details (parameters used, etc)
-3. ...assemble each step I did that day into a logical story line, that others can follow right as they see it, e.g.: *I observed X; I controlled for Y; Hypothesized explanation A; Falsified it; Came up with explanation B; Tested & proven it...*
-
-For all of the above, my solution is MarkDownLogs. I think its better than other solutions I found, like that combine source code with results. Most of people I interact with are not interested in the source code, but are very keen on seeing all kind of validations.
-
-#### It is better than existing report generators
-
-- Pure Markdown output, Simple and Elegant layout.
-- Integration with figures (linked to an external file & displayed: makes manual tailoring easy)
-- Easy generation of accurate figures (axis labels, etc) that are saved as a vector graphic (pdf): scalable for presentations, posters, etc
-- Named as source file + date: relate to the script, but avoid overwriting.
-- Does not spam your report with code, but its linked to it via its name, so you can look it up of if needed. (iPython notebook, KnittR)
-- Usable on GitHub Wiki's (although GitHub at the moment cannot)
-- Native export of tables from R to Markdown
-- Its all achieved in ~ 200 lines of well commented code.
-
-## Discover
-
-- See it working: Check out a dummy [R script](https://github.com/vertesy/MarkDownLogs/blob/master/Usage_Example_Script.R)
- and the [MarkDown report](https://github.com/vertesy/MarkDownLogs/blob/master/Usage_Example_Script/Usage_Example_Script.R.log.md)
- it generates inside this [GitHub Repo](https://github.com/vertesy/MarkDownLogs).
- - Check the function documentation in the [wiki](https://github.com/vertesy/MarkDownLogs/wiki)
-
-
-[*edit the website*](https://github.com/vertesy/MarkDownLogs/generated_pages/new)
\ No newline at end of file
diff --git a/Supplementary/Wiki.md b/Supplementary/Wiki.md
deleted file mode 100644
index 03f8cc0..0000000
--- a/Supplementary/Wiki.md
+++ /dev/null
@@ -1,51 +0,0 @@
-# Functions of the MarkDownLogger library
-...and some explanation...
-
-## Auxiliary functions
-
-1. ***kollapse***
- - parses (and prints) flexibly anything you pass on to it into a string
-- ***any_print***
- - more flexible printing fun
-- ***iround***
-- ***percentage_formatter***
-
-## Setup Logging
-
-1. ***create_set_OutDir***
- - # Defines and creates the Output / Reports directory, with a timestamped subfolder where you can backup manually.
-- ***setup_logging_markdown***
- - setup_logging file, path and modification date
-- ***continue_logging_markdown***
- - continue writing to an existing markdown file
-
-## Write into your markdown log file
-
-1. ***log_settings_MarkDown***
- - log your parameter settings into a tabular format
-- ***llprint***
- - log to markdown file and print to screen
-- ***llogit***
- - log to markdown file, do not print
-- ***MarkDown_ImgLink_formatter***
- - insert a link to a pdf image
-- ***MarkDown_Img_Logger_PDF_and_PNG***
- - insert 2 links, one for PDF, one for PNG version of the same image (png files are needed for web or email sharing!!!)
-- ***MarkDown_Img_Logger_4GitHub***
- - insert 2 links, one for PDF, one for PNG version of the same image (png files are needed for web or email sharing!!!)
-
-## Write out pretty tables to your markdown file
-
-1. ***MarkDown_Table_writer_DF_RowColNames***
-- ***MarkDown_Table_writer_NamedVector***
-
-## Generate and save plots into pdf and insert a diplay-link into your markdown file
-*All of them are based on the rfunction with the same name (without w prefix)*
-
-1. ***wplot***
-- ***whist***
-- ***wbarplot***
-- ***wboxplot***
-- ***wpie***
-- ***wplot_save_this***
- - This in a specific function: It saves the plot you created from the active device (in a pdf, with a link in the report if specified - as for all the above plotting functions).
\ No newline at end of file