jamba-package {jamba} | R Documentation |
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
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()
fordata.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, alsoshadowText_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 withlapply()
. -
pasteByRow()
,pasteByRowOrdered()
paste data.frame and matrix values by row, skipping blanks, optional factor order. -
rbindList()
convert list tomatrix
ordata.frame
. -
tcount()
extendstable()
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()
coloredkableExtra::kable()
output for 'Rmarkdown' -
setPrompt()
colored R prompt -
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 byprintDebug()
to maximize visual contrast, used withjam.lightMode
. -
jam.shadowColor
,jam.shadow.r
,jam.shadow.n
,jam.alphaShadow
,jam.outline
,jam.alphaOutline
to customize details forshadowText()
, seeshadowText_options()
for convenience.
Author(s)
Maintainer: James M. Ward jmw86069@gmail.com (ORCID) [copyright holder]
See Also
Useful links: