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.

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.

Author

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