Helper functions (control and parsing) for MarkdownReports and ggExpress.
It depends on:
... and provides functions for
You can install all of them directly from GitHub via devtools with one R command:
# install.packages("devtools"); # If you don't have it.
# Install dependencies
devtools::install_github(repo = "vertesy/Stringendo", upgrade = F)
devtools::install_github(repo = "vertesy/CodeAndRoll2", upgrade = F)
devtools::install_github(repo = "vertesy/ReadWriter", upgrade = F)
# Install MarkdownHelpers
devtools::install_github(repo = "vertesy/MarkdownHelpers", upgrade = F)
...then simply load the package:
require("MarkdownHelpers")Alternatively, you simply source it from the web. This way function help will not work, and you will have no local copy of the code on your hard drive.
source("https://raw.githubusercontent.com/vertesy/MarkdownHelpers/master/R/MarkdownHelpers.R")# It is best to load all dependencies:
require('Stringendo')
require('ReadWriter')
require('CodeAndRoll2')
require('MarkdownReports')
require('MarkdownHelpers')
MarkdownReports::setup_MarkdownReports()
# ------------------
"Used by other packages mostly"MarkdownReports and MarkdownHelpers works with such background variables defined by setup_MarkdownReports() in the global env .
(of connected functions)
flowchart LR
ww.ttl_field(ww.ttl_field) --> unless.specified(unless.specified)
ww.set.path_of_report(ww.set.path_of_report) --> ww.variable.and.path.exists(ww.variable.and.path.exists)
ww.set.mdlink(ww.set.mdlink) --> ww.variable.and.path.exists(ww.variable.and.path.exists)
ww.set.file.extension(ww.set.file.extension) --> unless.specified(unless.specified)
ww.set.PlotName(ww.set.PlotName) --> ww.autoPlotName(ww.autoPlotName)
wcolorize(wcolorize) --> color_check(color_check)
md.import.table(md.import.table) --> md.tableWriter.DF.w.dimnames(md.tableWriter.DF.w.dimnames)
md.import(md.import) --> ww.variable.and.path.exists(ww.variable.and.path.exists)
md.image.linker(md.image.linker) --> unless.specified(unless.specified)
md.image.linker(md.image.linker) --> llogit(llogit)
md.LogSettingsFromList(md.LogSettingsFromList) --> md.tableWriter.DF.w.dimnames(md.tableWriter.DF.w.dimnames)
md.List2Table(md.List2Table) --> md.tableWriter.DF.w.dimnames(md.tableWriter.DF.w.dimnames)
md.LinkTable(md.LinkTable) --> md.tableWriter.DF.w.dimnames(md.tableWriter.DF.w.dimnames)
lookup(lookup) --> llprint(llprint)
llwrite_list(llwrite_list) --> llogit(llogit)
llwrite_list(llwrite_list) --> llprint(llprint)
filter_survival_length(filter_survival_length) --> llprint(llprint)
filter_MidPass(filter_MidPass) --> ww.variable.and.path.exists(ww.variable.and.path.exists)
filter_MidPass(filter_MidPass) --> llogit(llogit)
filter_LP(filter_LP) --> ww.variable.and.path.exists(ww.variable.and.path.exists)
filter_LP(filter_LP) --> llogit(llogit)
llogit(llogit) --> ww.variable.and.path.exists(ww.variable.and.path.exists)
filter_HP(filter_HP) --> ww.variable.and.path.exists(ww.variable.and.path.exists)
filter_HP(filter_HP) --> llogit(llogit)
llprint(llprint) --> ww.variable.and.path.exists(ww.variable.and.path.exists)
combine.matrices.by.rowname.intersect(combine.matrices.by.rowname.intersect) --> llprint(llprint)
ww.FnP_parser(ww.FnP_parser) --> ww.set.OutDir(ww.set.OutDir)
color_check(color_check) --> ww.FnP_parser(ww.FnP_parser)
created by convert_igraph_to_mermaid()
Updated: 2024/10/24 16:04
irequire. Load a package. If it does not exist, try to install it from CRAN.
unless.specified. Return value X (TRUE by default) unless the variable is defined. If defined, it returns the variable.
TRUE.unless. Return TRUE unless the variable is defined. If defined, it returns the value of the variable.
FALSE.unless. Return FALSE unless the variable is defined. If defined, it returns the value of the variable.
lookup. Awesome pattern matching for a set of values in another set of values. Returns a list with all kinds of results.
combine.matrices.by.rowname.intersect. Combine two matrices by their rownames intersect.
ww.variable.and.path.exists. Check if a variable name is defined, and if so, does the path (to a file) stored in that variable points to an existing directory?
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 "path_of_report" variable is defined.
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 "path_of_report" variable is defined. It does not print the sentence to the screen.
md.write.as.list. Writes a vector as a (numbered) list into the report file.
md.image.linker. Format a markdown image reference (link) to a .pdf and .png versions of graph, and insert both links to the markdown report, set by "path_of_report". If the "b.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.
llwrite_list. Print a list object from R, one element per line, into your markdown report
md.import. Import and concatenated an external markdown or text file to the report
md.LogSettingsFromList. Log the parameters & settings used in the script and stored in a list, in a table format in the report.
md.List2Table. Broader variant of md.LogSettingsFromList(). Log the values (col2) from a named (col1) list, in a table format in the report.
md.tableWriter.DF.w.dimnames. 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 "path_of_report".
md.tableWriter.VEC.w.names. Take an R vector with names, parse a markdown table from it, and write it to the markdown report, set by "path_of_report".
md.LinkTable. Take a dataframe where every entry is a string containing an html link, parse and write out. a properly formatted markdown table.
md.import.table. Import a table (.csv, or tab seprated values, .tsv file) and write it in markdown format to the report.
filter_HP. Filter values that fall between above high-pass-threshold (X >).
filter_LP. Filter values that fall below the low-pass threshold (X <).
filter_MidPass. Filter values that fall above high-pass-threshold !(X >= )! and below the low-pass threshold (X <).
ww.FnP_parser. Internal Function. Parses the full path from the filename & location of the file.
ww.variable.and.path.exists. Check if a variable name is defined, and if so, does the path (to a file) stored in that variable points to an existing directory?
ww.variable.exists.and.true. Check if a variable name is defined, and if so, is it TRUE
ww.set.OutDir. Checks if global variable OutDir is defined. If not, it returns the current working directory
ww.set.path_of_report. Checks if global variable path_of_report is defined. If not, it defines it as Analysis.md in the current working directory @importFrom Stringendo iprint @examples ww.set.path_of_report()
ww.set.PlotName. Generates a plotname (use if none is specified) @importFrom Stringendo iprint @examples ww.set.PlotName()
ww.set.mdlink. Internal function. Sets inserting a markdown link to the image (created by the wplot* function that calls this function) only if 'path_of_report' is defined and 'b.mdlink' is defined as TRUE.
ww.md.image.link.parser. 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. ww.md.image.link.parser(Directory, "MyImage.png").
ww.ttl_field. Internal function. Creates the string written into the PDF files "Title' (metadata) field.
ww.autoPlotName. Internal function. Creates automatic plot and file-names.
ww.assign_to_global. A function loading results to the global environment. Source: https://stackoverflow.com/questions/28180989/
try.dev.off. Tries to close R graphical devices without raising an error.
jjpegA4. Setup an A4 size jpeg.
color_check. Display the colors encoded by the numbers / color-ID-s you pass on to this function
wcolorize. Generate color palettes. Input: a vector with categories, can be numbers or strings. Handles repeating values. Output: color vector of equal length as input. Optionally it can ouput a list where an extra element lists the categories (simply using unique would remove the names). See example. Some color scale depend on packages "colorRamps", or "gplots".
filter_survival_length. Parse a sentence reporting the % of filter survival.
In 2021, function libraries got reorganized as below:
