Function reference • jamba

Sort functions Functions based upon alphanumeric sorting
`mixedOrder()`	order alphanumeric values keeping numeric values in proper order
`mixedSort()`	sort alphanumeric values keeping numeric values in proper order
`mixedSortDF()`	sort data.frame keeping numeric values in proper order
`mixedSorts()`	sort alphanumeric values within a list format
`mmixedOrder()`	order alphanumeric values from a list
Grep functions Convenient grep functions for speed of re-use
`grepls()`	Search for objects in the environment
`igrep()`	case-insensitive grep
`igrepHas()`	vector contains any case-insensitive grep match
`igrepl()`	case-insensitive logical grepl
`provigrep()` `proigrep()`	provigrep: progressive case-insensitive value-grep
`unigrep()`	case-insensitive grep, returning unmatched indices
`unvigrep()`	case-insensitive grep, returning unmatched values
`vgrep()`	grep, returning values
`vigrep()`	case-insensitive grep, returning values
Plot functions Functions that assist with R plotting
`adjustAxisLabelMargins()`	Adjust axis label margins
`coordPresets()`	Process coordinate adjustment presets
`decideMfrow()`	Decide plot panel rows, columns for par(mfrow)
`drawLabels()`	Draw text labels on a base R plot
`getPlotAspect()`	Get aspect ratio for coordinates, plot, or device
`groupedAxis()`	Draw grouped axis labels
`imageByColors()`	Display color raster image using a matrix of colors
`imageDefault()`	Display a color raster image
`minorLogTicksAxis()`	Display major and minor tick marks for log-scale axis
`nullPlot()`	Create a blank plot with optional labels
`plotPolygonDensity()`	Plot distribution and histogram overlay
`plotRidges()`	Plot ridges density plots for numeric matrix input
`plotSmoothScatter()`	Smooth scatter plot with enhancements
`shadowText()`	Draw text with shadow border
`shadowText_options()`	Get and set options for shadowText
`showColors()`	Show colors from a vector or list
`smoothScatterJam()`	Smooth scatter plot, Jam style
`sqrtAxis()`	Determine square root axis tick mark positions
`usrBox()`	Draw colored box indicating R plot space
Color functions Functions that manipulate colors
`alpha2col()`	set R color alpha value
`applyCLrange()`	Apply CL color range
`col2alpha()`	get R color alpha value
`col2hcl()`	convert R color to HCL color matrix
`col2hsl()`	convert R color to HSL color matrix
`col2hsv()`	Convert R color to HSV matrix
`color2gradient()`	Make a color gradient
`fixYellow()`	Fix yellow color
`fixYellowHue()`	Fix yellow color hue
`getColorRamp()`	get color ramp by name, color, or function
`hcl2col()`	convert HCL to R color
`hsl2col()`	convert HCL to R color
`hsv2col()`	Convert HSV matrix to R color
`isColor()`	detect valid R color
`kable_coloring()`	Extend kableExtra colorization of Rmarkdown tables
`makeColorDarker()`	make R colors darker (or lighter)
`make_html_styles()`	vectorized make_styles for html span output
`make_styles()`	vectorized make_styles for crayon output
`rgb2col()`	Convert RGB color matrix to R color
`setCLranges()`	Get Chroma and Luminance ranges for the given lightMode
`setTextContrastColor()`	Define visible text color
`showColors()`	Show colors from a vector or list
`unalpha()`	Remove alpha transparency from colors
`warpRamp()`	Warp colors in a color ramp
String functions Functions which sort or manipulate character strings
`asSize()`	convert numeric value to size
`breaksByVector()`	break a vector into groups
`cPaste()`	paste a list into a delimited vector
`cPasteS()`	paste a list into a delimited vector using sorted values
`cPasteSU()`	paste a list into a delimited vector using sorted, unique values
`cPasteU()`	paste a list into a delimited vector using unique values
`cPasteUnique()`	paste a list into a delimited vector using unique values
`fillBlanks()`	Fill blank entries in a vector
`formatInt()`	Format an integer as a string
`gsubOrdered()`	Global substitution into ordered factor
`gsubs()`	Pattern replacement with multiple patterns
`makeNames()`	make unique vector names
`mixedOrder()`	order alphanumeric values keeping numeric values in proper order
`mixedSort()`	sort alphanumeric values keeping numeric values in proper order
`mixedSortDF()`	sort data.frame keeping numeric values in proper order
`mixedSorts()`	sort alphanumeric values within a list format
`mmixedOrder()`	order alphanumeric values from a list
`nameVector()`	assign unique names for a vector
`nameVectorN()`	define a named vector using vector names
`padInteger()`	prefix integers with leading zeros
`padString()`	pad a character string to a fixed length
`pasteByRow()`	Paste data.frame rows into character vector
`pasteByRowOrdered()`	Paste data.frame rows into an ordered factor
`sizeAsNum()`	convert size to numeric value
`tcount()` `tcount2()`	frequency of entries, ordered by frequency
`ucfirst()`	Uppercase the first letter in each word
`uniques()`	apply unique to each element of a list
Numeric functions Functions which manipulate numeric data
`deg2rad()`	Convert degrees to radians
`fix_matrix_ratio()`	Fix matrix dimension ratio
`noiseFloor()`	Apply noise floor and ceiling to numeric vector
`normScale()`	Scale a numeric vector from 0 to 1
`rad2deg()`	Convert radians to degrees
`rowGroupMeans()` `rowGroupRmOutliers()`	Calculate row group means, or other statistics
`rowRmMadOutliers()`	Remove outlier points per row by MAD factor threshold
`warpAroundZero()`	Warp a vector of numeric values relative to zero
List functions Functions which manipulate list objects
`cPaste()`	paste a list into a delimited vector
`cPasteS()`	paste a list into a delimited vector using sorted values
`cPasteSU()`	paste a list into a delimited vector using sorted, unique values
`cPasteU()`	paste a list into a delimited vector using unique values
`cPasteUnique()`	paste a list into a delimited vector using unique values
`heads()`	Apply head() across each element in a list of vectors
`jam_rapply()`	Jam-specific recursive apply
`list2df()`	Convert list of vectors to data.frame with item, value, name
`mergeAllXY()`	Merge list of data.frames retaining all rows
`mixedSorts()`	sort alphanumeric values within a list format
`rbindList()`	rbind a list of vectors into matrix or data.frame
`relist_named()`	relist a vector which allows re-ordered names
`rlengths()`	lengths for recursive lists
`sclass()`	return the classes of a list of objects
`sdim()` `sdima()` `ssdima()` `ssdim()`	print dimensions of list object elements
`uniques()`	apply unique to each element of a list
`unnestList()`	Un-nest a nested list into a simple list
Date functions Functions which manipulate date objects or strings
`asDate()`	convert date DDmmmYYYY to Date
`dateToDaysOld()`	convert date to age in days
`getDate()`	get simple date string
Export functions Practical functions for exporting data, e.g. to Excel xlsx
`applyXlsxCategoricalFormat()`	Add categorical colors to Excel xlsx worksheets
`applyXlsxConditionalFormat()`	Xlsx Conditional formatting
`readOpenxlsx()`	Import one or more data.frame from Excel xlsx format
`set_xlsx_colwidths()`	Set column widths in Xlsx files
`set_xlsx_rowheights()`	Set row heights in Xlsx files
`writeOpenxlsx()`	Export a data.frame to Excel xlsx format
Utility functions Functions that enhance utility of other existing functions or packages
`call_fn_ellipsis()`	Safely call a function using ellipsis
`reload_rmarkdown_cache()`	Reload Rmarkdown cache
Heatmap functions Specific enhancements for `ComplexHeatmap::Heatmap()`
`cell_fun_label()`	ComplexHeatmap cell function to label heatmap cells
`heatmap_column_order()`	Return Heatmap column order from ComplexHeatmap heatmap object
`heatmap_row_order()`	Return Heatmap row order from ComplexHeatmap heatmap object
Practical functions Practical functions to enhance routine R work, essentially miscellaneous
`breakDensity()`	Calculate more detailed density of numeric values
`checkLightMode()`	check lightMode for light background color
`check_pkg_installed()`	Lightweight method to check if an R package is installed
`colNum2excelName()`	convert column number to Excel column name
`color_dither()`	Make dithered color pattern light-dark
`diff_functions()`	Compare two functions line by line using diff
`exp2signed()`	exponentiate log2 values with directionality
`fileInfo()`	file information in data.frame format
`fixYellow()`	Fix yellow color
`getAxisLabel()`	Get axis label for minorLogTicks
`handleArgsText()`	Handle function arguments as text
`heads()`	Apply head() across each element in a list of vectors
`isFALSEV()`	Vectorized isFALSE
`isTRUEV()`	Vectorized isTRUE
`jamba`	jamba: Jam Base Methods
`jargs()`	Show R function arguments jam-style
`kable_coloring()`	Extend kableExtra colorization of Rmarkdown tables
`lldf()`	Long listing of R session objects
`log2signed()`	log2 transformation with directionality
`make_html_styles()`	vectorized make_styles for html span output
`make_styles()`	vectorized make_styles for crayon output
`match_unique()`	Match unique vector values against itself
`mergeAllXY()`	Merge list of data.frames retaining all rows
`middle()`	Return the middle portion of data similar to head and tail
`minorLogTicks()`	Calculate major and minor tick marks for log-scale axis
`newestFile()`	Return the newest file from a vector of files
`printDebug()` `printDebugI()` `printDebugHtml()`	print colorized output to R console
`renameColumn()`	Rename columns in a data.frame, matrix, tibble, or GRanges object
`rmInfinite()`	remove Infinite values
`rmNA()`	remove NA values
`rmNAs()`	remove NA values from list elements
`rmNULL()`	remove NULL entries from list
`sclass()`	return the classes of a list of objects
`sdim()` `sdima()` `ssdima()` `ssdim()`	print dimensions of list object elements
`setPrompt()`	set R prompt with project name and R version
Internal functions Functions typically for internal use by other Jam functions
`jamCalcDensity()`	Calculate scatter plot point density

Reference

Sort functions

Grep functions

Plot functions

Color functions

String functions

Numeric functions

List functions

Date functions

Export functions

Utility functions

Heatmap functions

Practical functions

Internal functions