# Just Analysis Methods Base

## Documentation for package ‘jamba’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I J K L M N P R S T U V W

## -- 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 --

exp2signed | 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 --

kable_coloring | 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 --

tcount | 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