Just Analysis Methods Base

Documentation for package ‘jamba’ version 1.0.4

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-- A --

adjustAxisLabelMargins	Adjust axis label margins
alpha2col	set R color alpha value
applyCLrange	Apply CL color range
applyXlsxCategoricalFormat	Add categorical colors to 'Excel' 'xlsx' worksheets
applyXlsxConditionalFormat	Xlsx Conditional formatting
asDate	convert date DDmmmYYYY to Date
asSize	convert numeric value or R object to human-readable size

-- B --

breakDensity	Calculate more detailed density of numeric values
breaksByVector	break a vector into groups

-- C --

call_fn_ellipsis	Safely call a function using ellipsis
cell_fun_label	ComplexHeatmap cell function to label heatmap cells
checkLightMode	check lightMode for light background color
check_pkg_installed	Lightweight method to check if an R package is installed
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
colNum2excelName	convert column number to 'Excel' column name
color2gradient	Make a color gradient
color_dither	Make dithered color pattern light-dark
coordPresets	Process coordinate adjustment presets
cPaste	paste a list into a delimited vector
cPasteS	paste a list into a delimited vector
cPasteSU	paste a list into a delimited vector
cPasteU	paste a list into a delimited vector
cPasteUnique	paste a list into a delimited vector

-- D --

dateToDaysOld	convert date to age in days
decideMfrow	Decide plot panel rows, columns for graphics::par(mfrow)
deg2rad	Convert degrees to radians
drawLabels	Draw text labels on a base R plot

-- E --

exponentiate log2 values with directionality

-- F --

fillBlanks	Fill blank entries in a vector
fixYellow	Fix yellow color
fixYellowHue	Fix yellow color hue
formatInt	Format an integer as a string

-- G --

getAxisLabel	Get axis label for minorLogTicks
getColorRamp	get color ramp by name, color, or function
getDate	get simple date string
getPlotAspect	Get aspect ratio for coordinates, plot, or device
grepls	Search for objects in the environment
groupedAxis	Draw grouped axis labels
gsubOrdered	Global substitution into ordered factor
gsubs	Pattern replacement with multiple patterns

-- H --

handleArgsText	Handle function arguments as text
hcl2col	convert HCL to R color
heads	Apply head() across each element in a list of vectors
heatmap_column_order	Return Heatmap column order from ComplexHeatmap heatmap object
heatmap_row_order	Return Heatmap row order from ComplexHeatmap heatmap object
hsl2col	convert HCL to R color
hsv2col	Convert HSV matrix to R color

-- I --

igrep	case-insensitive grep
igrepHas	vector contains any case-insensitive grep match
igrepl	case-insensitive logical grepl
imageByColors	Display color raster image using a matrix of colors
imageDefault	Display a color raster image
isColor	detect valid R color
isFALSEV	Vectorized isFALSE
isTRUEV	Vectorized isTRUE

-- J --

jamCalcDensity	Calculate scatter plot point density
jam_rapply	Jam-specific recursive apply
jargs	Show R function arguments jam-style

-- K --

Extend kableExtra colorization of 'Rmarkdown' tables

-- L --

list2df	Convert list of vectors to data.frame with item, value, name
lldf	Long listing of R session objects
log2signed	log2 transformation with directionality
logFoldAxis	Display major and minor tick marks for log-scale axis

-- M --

makeColorDarker	make R colors darker (or lighter)
makeNames	make unique vector names
make_html_styles	vectorized make_styles for html span output
make_styles	vectorized make_styles for crayon output
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
minorLogTicksAxis	Display major and minor tick marks for log-scale axis
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

-- N --

nameVector	assign unique names for a vector
nameVectorN	define a named vector using vector names
newestFile	Return the newest file from a vector of files
noiseFloor	Apply noise floor and ceiling to numeric vector
normScale	Scale a numeric vector from 0 to 1
nullPlot	Create a blank plot with optional labels

-- P --

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
plotPolygonDensity	Plot distribution and histogram overlay
plotRidges	Plot ridges density plots for numeric matrix input
plotSmoothScatter	Smooth scatter plot with enhancements
printDebug	print colorized output to R console
printDebugHtml	print colorized output to R console
printDebugI	print colorized output to R console
proigrep	provigrep: progressive case-insensitive value-grep
provigrep	provigrep: progressive case-insensitive value-grep
pvalueAxis	Display major and minor tick marks for log-scale axis

-- R --

rad2deg	Convert radians to degrees
rainbow2	Simple rainbow palette replacement
rbindList	rbind a list of vectors into matrix or data.frame
readOpenxlsx	Import one or more data.frame from 'Excel' 'xlsx' format
relist_named	relist a vector which allows re-ordered names
reload_rmarkdown_cache	Reload 'Rmarkdown' cache
renameColumn	Rename columns in a data.frame, matrix, tibble, or GRanges object
rgb2col	Convert RGB color matrix to R color
rlengths	lengths for recursive lists
rmInfinite	remove Infinite values
rmNA	remove NA values
rmNAs	remove NA values from list elements
rmNULL	remove NULL entries from list
rowGroupMeans	Calculate row group means, or other statistics
rowGroupRmOutliers	Calculate row group means, or other statistics
rowRmMadOutliers	Remove outlier points per row by MAD factor threshold

-- S --

sclass	return the classes of a list of objects
sdim	print dimensions of list object elements
sdima	print dimensions of list object elements
setCLranges	Get Chroma and Luminance ranges for the given lightMode
setPrompt	set R prompt with project name and R version
setTextContrastColor	Define visible text color
set_xlsx_colwidths	Set column widths in Xlsx files
set_xlsx_rowheights	Set row heights in Xlsx files
shadowText	Draw text with shadow border
shadowText_options	Get and set options for shadowText
showColors	Show colors from a vector or list
sizeAsNum	convert size to numeric value
smoothScatterJam	Smooth scatter plot, Jam style
sqrtAxis	Determine square root axis tick mark positions
ssdim	print dimensions of list object elements
ssdima	print dimensions of list object elements

-- T --

frequency of entries, ordered by frequency

-- U --

ucfirst	Uppercase the first letter in each word
unalpha	Remove alpha transparency from colors
unigrep	case-insensitive grep, returning unmatched indices
uniques	apply unique to each element of a list
unnestList	Un-nest a nested list into a simple list
unvigrep	case-insensitive grep, returning unmatched values
usrBox	Draw colored box indicating R plot space

-- V --

vgrep	grep, returning values
vigrep	case-insensitive grep, returning values

-- W --

warpAroundZero	Warp a vector of numeric values relative to zero
warpRamp	Warp colors in a color ramp
writeOpenxlsx	Export a data.frame to 'Excel' 'xlsx' format