Package index • jamba

mixedSort 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 graphics::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() logFoldAxis() pvalueAxis(): 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

sqrtAxis(): Determine square root axis tick mark positions

usrBox(): Draw colored box indicating R plot space

Numeric functions

Functions which manipulate numeric data

deg2rad(): Convert degrees to radians

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

String functions

Functions which sort or manipulate character strings

asSize(): convert numeric value or R object to human-readable size

breaksByVector(): break a vector into groups

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

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(): frequency of entries, ordered by frequency

ucfirst(): Uppercase the first letter in each word

List functions

Functions which manipulate list objects

cPaste() cPasteS() cPasteSU() cPasteUnique() cPasteU(): paste a list into a delimited vector

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

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)

rainbow2(): Simple rainbow palette replacement

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

Export functions

Exporting data in xlsx format

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

Practical functions

Practical functions to enhance routine R work, miscellaneous

breakDensity(): Calculate more detailed density of numeric values

call_fn_ellipsis(): Safely call a function using ellipsis

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

exp2signed(): exponentiate log2 values with directionality

getAxisLabel(): Get axis label for minorLogTicks

isFALSEV(): Vectorized isFALSE

isTRUEV(): Vectorized isTRUE

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

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

reload_rmarkdown_cache(): Reload 'Rmarkdown' cache

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

setPrompt(): set R prompt with project name and R version

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

Internal functions

Functions typically for internal use by other Jam functions

handleArgsText(): Handle function arguments as text

jamCalcDensity(): Calculate scatter plot point density

make_html_styles(): vectorized make_styles for html span output

make_styles(): vectorized make_styles for crayon output

smoothScatterJam(): Smooth scatter plot, Jam style