jamba-package

jamba: Jam Base Methods

The jamba package contains several jam base functions which are re-usable for routine R analysis work, and are important dependencies for other Jam R packages. package

Details

See the function reference for a complete list of functions.

The goal is to implement methods as lightweight as possible, so so inclusion in an analysis workflow will not incur a noticeable burden.

plot functions

• plotSmoothScatter() smoothScatter() enhanced for more visual detail
• imageDefault() enhanced rasterized image() with fixed aspect ratio
• imageByColors() for data.frame of colors and optional labels centered across repeated values.
• showColors() color display for vector, list, color function, or mixed formats.
• nullPlot() blank plot that labels the current margin sizes
• minorLogTicksAxis() log-scale axis ticks in base R with custom log base, optional offset, e.g. log2(1 + x)
• shadowText() base R text labels with shadow or outline or both, also shadowText_options().
• getPlotAspect(), decideMfrow() convenience base R graphics.

string functions

• mixedSort(), mixedOrder(), mixedSortDF() - efficient alphanumeric "version" sort, with options helpful for gene symbols.
• vgrep(), vigrep(), igrep(), vigrep() fast grep wrappers for value-return, case-insensitive search.
• provigrep(), proigrep() - progressive, ordered grep to use pattern matching to re-order a vector.
• makeNames() create unique, versioned names with custom format
• nameVector() apply names to vector dynamically
• nameVectorN() vector of named names useful with lapply().
• pasteByRow(), pasteByRowOrdered() paste data.frame and matrix values by row, skipping blanks, optional factor order.
• rbindList() convert list to matrix or data.frame.
• tcount() extends table() to sort by size and optional minimum count filter.

color functions

• rgb2col(), col2hcl(), col2hcl(), col2hsv(), hsv2col() color interconversion
• setTextContrastColor() text contrast color per given background color
• getColorRamp() catch-all to get named gradients, or expand one or more colors to gradient.
• makeColorDarker(), color2gradient(), showColors() color manipulation and display

miscellaneous helper functions

• printDebug() colored text output to console, 'Rmarkdown', HTML
• kable_coloring() colored kableExtra::kable() output for 'Rmarkdown'
• setPrompt() colored R prompt
• deg2rad(), rad2deg() interconvert degrees to radians.
• getDate(), asDate(), dateToDaysOld() human-readable, opinionated date formatting
• padString(), padInteger() pad character or integer strings
• rmNA(), rmNULL(), rmInfinite() remove or replace missing or NA values with defined alternatives

export and import functions

• readOpenxlsx() import worksheets from 'xlsx' 'Excel' files.
• writeOpenxlsx() export worksheets to 'xlsx' 'Excel' files with color, formatting, and styling.

Jam options

The jamba package recognizes some global options, but limits these options to include only non-analysis options. For example, no global option should change the numerical manipulation of data.

• jam.lightMode - logical whether the R console or graphical background is light or dark, printDebug() limits the luminance range to maximize visual contrast.

• jam.Crange,jam.Lrange - numerical values used by printDebug()

  to maximize visual contrast, used with jam.lightMode.

• jam.shadowColor,jam.shadow.r,jam.shadow.n,jam.alphaShadow, jam.outline,jam.alphaOutline to customize details for shadowText(), see shadowText_options() for convenience.

See Also

Useful links:

• https://jmw86069.github.io/jamba/
• Report bugs at https://github.com/jmw86069/jamba/issues

Author(s)

Maintainer : James M. Ward jmw86069@gmail.com (ORCID) [copyright holder]