MarkdownHelpers

Helper functions (control and parsing) for MarkdownReports and ggExpress.

Installation

It depends on:

• Stringendo
• ReadWriter
• CodeAndRoll2

... and provides functions for

• MarkdownReports
• ggExpress
• Seurat.utils
• Seurat.pipeline

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")

Usage

# 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"

Most MarkdownHelpers function write into a markdown file.

That file is defined in path_of_report, by first calling MarkdownReports::setup_MarkdownReports().

MarkdownReports and MarkdownHelpers works with such background variables defined by setup_MarkdownReports() in the global env .

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Function relationships

(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()

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List of Functions (38)

Updated: 2023/11/24 16:40

• 1 stopif()

  stopif. Stop script if the condition is met, and print a message

• 2 irequire()

  irequire. Load a package. If it does not exist, try to install it from CRAN.

• 3 unless.specified()

  unless.specified. Return value X (TRUE by default) unless the variable is defined. If defined, it returns the variable.

• 4 TRUE.unless()

  TRUE.unless. Return TRUE unless the variable is defined. If defined, it returns the value of the variable.

• 5 FALSE.unless()

  FALSE.unless. Return FALSE unless the variable is defined. If defined, it returns the value of the variable.

• 6 lookup()

  lookup. Awesome pattern matching for a set of values in another set of values. Returns a list with all kinds of results.

• 7 combine.matrices.by.rowname.intersect()

  combine.matrices.by.rowname.intersect. Combine two matrices by their rownames intersect.

• 8 ww.variable.and.path.exists()

  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?

• 9 llprint()

  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.

• 10 llogit()

  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.

• 11 md.write.as.list()

  md.write.as.list. Writes a vector as a (numbered) list into the report file.

• 12 md.image.linker()

  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.

• 13 llwrite_list()

  llwrite_list. Print a list object from R, one element per line, into your markdown report

• 14 md.import()

  md.import. Import and concatenated an external markdown or text file to the report

• 15 md.LogSettingsFromList()

  md.LogSettingsFromList. Log the parameters & settings used in the script and stored in a list, in a table format in the report.

• 16 md.List2Table()

  md.List2Table. Broader variant of md.LogSettingsFromList(). Log the values (col2) from a named (col1) list, in a table format in the report.

• 17 md.tableWriter.DF.w.dimnames()

  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".

• 18 md.tableWriter.VEC.w.names()

  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".

• 19 md.LinkTable()

  md.LinkTable. Take a dataframe where every entry is a string containing an html link, parse and write out. a properly formatted markdown table.

• 20 md.import.table()

  md.import.table. Import a table (.csv, or tab seprated values, .tsv file) and write it in markdown format to the report.

• 21 filter_HP()

  filter_HP. Filter values that fall between above high-pass-threshold (X >).

• 22 filter_LP()

  filter_LP. Filter values that fall below the low-pass threshold (X <).

• 23 filter_MidPass()

  filter_MidPass. Filter values that fall above high-pass-threshold !(X >= )! and below the low-pass threshold (X <).

• 24 ww.variable.and.path.exists()

  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?

• 25 ww.variable.exists.and.true()

  ww.variable.exists.and.true. Check if a variable name is defined, and if so, is it TRUE

• 26 ww.set.OutDir()

  ww.set.OutDir. Checks if global variable OutDir is defined. If not, it returns the current working directory

• 27 ww.set.path_of_report()

  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

• 28 ww.set.PlotName()

  ww.set.PlotName. Generates a plotname (use if none is specified)

• 29 ww.set.mdlink()

  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.

• 30 ww.md.image.link.parser()

  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").

• 31 ww.ttl_field()

  ww.ttl_field. Internal function. Creates the string written into the PDF files "Title' (metadata) field.

• 32 ww.autoPlotName()

  ww.autoPlotName. Internal function. Creates automatic plot and file-names.

• 33 ww.assign_to_global()

  ww.assign_to_global. A function loading results to the global environment. Source: https://stackoverflow.com/questions/28180989/

• 34 try.dev.off()

  try.dev.off. Tries to close R graphical devices without raising an error.

• 35 jjpegA4()

  jjpegA4. Setup an A4 size jpeg.

• 36 wcolorize()

  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".

• 37 color_check()

  color_check. Display the colors encoded by the numbers / color-ID-s you pass on to this function

• 38 filter_survival_length()

  filter_survival_length. Parse a sentence reporting the % of filter survival.

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In 2021, function libraries got reorganized as below: