jamba-package: jamba: Jam Base Methods

In jmw86069/jamba: Just Analysis Methods Base

jamba: Jam Base Methods

Description

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.

Details

The goal will be to maintain these methods as lightweight as possible, so their 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.

• 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.

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.

Author(s)

Maintainer: James M. Ward [e-mail] [copyright holder]

See Also

Useful links:

• https://jmw86069.github.io/jamba/

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

jmw86069/jamba documentation built on Feb. 28, 2025, 9:07 p.m.