Package: jamba 1.0.2

James M. Ward

jamba: Just Analysis Methods Base

Just analysis methods ('jam') base functions focused on bioinformatics. Version- and gene-centric alphanumeric sort, unique name and version assignment, colorized console and 'HTML' output, color ramp and palette manipulation, 'Rmarkdown' cache import, styled 'Excel' worksheet import and export, interpolated raster output from smooth scatter and image plots, list to delimited vector, efficient list tools.

Authors:James M. Ward [aut, cre, cph]

jamba_1.0.2.tar.gz
jamba_1.0.2.tar.gz(r-4.5-noble)jamba_1.0.2.tar.gz(r-4.4-noble)
jamba_1.0.2.tgz(r-4.4-emscripten)jamba_1.0.2.tgz(r-4.3-emscripten)
jamba.pdf |jamba.html✨
jamba/json (API)
NEWS

# Install 'jamba' in R:

install.packages('jamba', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jmw86069/jamba/issues

Pkgdown site:https://jmw86069.github.io

On CRAN:

2.70 score 143 exports 4 dependencies

Last updated 1 hours agofrom:48151963fb. Checks:3 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 10 2025
R-4.5-linux	OK	Mar 10 2025
R-4.4-linux	OK	Mar 10 2025

Exports:adjustAxisLabelMargins alpha2col applyCLrange applyXlsxCategoricalFormat applyXlsxConditionalFormat asDate asSize breakDensity breaksByVector call_fn_ellipsis cell_fun_label check_pkg_installed checkLightMode col2alpha col2hcl col2hsl col2hsv colNum2excelName color_dither color2gradient coordPresets cPaste cPasteS cPasteSU cPasteU cPasteUnique dateToDaysOld decideMfrow deg2rad drawLabels exp2signed fillBlanks fixYellow fixYellowHue formatInt getAxisLabel getColorRamp getDate getPlotAspect grepls groupedAxis gsubOrdered gsubs handleArgsText hcl2col heads heatmap_column_order heatmap_row_order hsl2col hsv2col igrep igrepHas igrepl imageByColors imageDefault isColor isFALSEV isTRUEV jam_rapply jamCalcDensity jargs kable_coloring list2df lldf log2signed logFoldAxis make_html_styles make_styles makeColorDarker makeNames mergeAllXY middle minorLogTicks minorLogTicksAxis mixedOrder mixedSort mixedSortDF mixedSorts mmixedOrder nameVector nameVectorN newestFile noiseFloor normScale nullPlot padInteger padString pasteByRow pasteByRowOrdered plotPolygonDensity plotRidges plotSmoothScatter printDebug printDebugHtml printDebugI proigrep provigrep pvalueAxis rad2deg rainbow2 rbindList readOpenxlsx relist_named reload_rmarkdown_cache renameColumn rgb2col rlengths rmInfinite rmNA rmNAs rmNULL rowGroupMeans rowGroupRmOutliers rowRmMadOutliers sclass sdim sdima set_xlsx_colwidths set_xlsx_rowheights setCLranges setPrompt setTextContrastColor shadowText shadowText_options showColors sizeAsNum smoothScatterJam sqrtAxis ssdim ssdima tcount ucfirst unalpha unigrep uniques unnestList unvigrep usrBox vgrep vigrep warpAroundZero warpRamp writeOpenxlsx

Dependencies:colorspace KernSmooth RColorBrewer withr

Jamba Overview

James M. Ward

Rendered fromjamba-vignette.Rmdusingknitr::rmarkdownon Mar 10 2025.

Last update: 2025-03-10
Started: 2025-03-10

Citation

Farris S, Ward JM, Carstens KE, Samadi M, Wang Y, Dudek SM (2019). “Hippocampal Subregions Express Distinct Dendritic Transcriptomes that Reveal Differences in Mitochondrial Function in CA2.” Cell Reports, 29(2), 522-539. doi:10.1016/j.celrep.2019.08.093.

Corresponding BibTeX entry:

  @Article{,
    title = {Hippocampal Subregions Express Distinct Dendritic
      Transcriptomes that Reveal Differences in Mitochondrial Function
      in CA2},
    author = {Shannon Farris and James M. Ward and Kelly E. Carstens
      and Mahsa Samadi and Yu Wang and Serena M. Dudek},
    year = {2019},
    journal = {Cell Reports},
    volume = {29},
    number = {2},
    pages = {522-539},
    doi = {10.1016/j.celrep.2019.08.093},
  }

Readme and manuals

Help Manual

Help page	Topics
Adjust axis label margins	adjustAxisLabelMargins
set R color alpha value	alpha2col
Apply CL color range	applyCLrange
Add categorical colors to 'Excel' 'xlsx' worksheets	applyXlsxCategoricalFormat
Xlsx Conditional formatting	applyXlsxConditionalFormat
convert date DDmmmYYYY to Date	asDate
convert numeric value or R object to human-readable size	asSize
Calculate more detailed density of numeric values	breakDensity
break a vector into groups	breaksByVector
Safely call a function using ellipsis	call_fn_ellipsis
ComplexHeatmap cell function to label heatmap cells	cell_fun_label
Lightweight method to check if an R package is installed	check_pkg_installed
check lightMode for light background color	checkLightMode
get R color alpha value	col2alpha
convert R color to HCL color matrix	col2hcl
convert R color to HSL color matrix	col2hsl
Convert R color to HSV matrix	col2hsv
convert column number to 'Excel' column name	colNum2excelName
Make dithered color pattern light-dark	color_dither
Make a color gradient	color2gradient
Process coordinate adjustment presets	coordPresets
paste a list into a delimited vector	cPaste cPasteS cPasteSU cPasteU cPasteUnique
convert date to age in days	dateToDaysOld
Decide plot panel rows, columns for graphics::par(mfrow)	decideMfrow
Convert degrees to radians	deg2rad
Draw text labels on a base R plot	drawLabels
exponentiate log2 values with directionality	exp2signed
Fill blank entries in a vector	fillBlanks
Fix yellow color	fixYellow
Fix yellow color hue	fixYellowHue
Format an integer as a string	formatInt
Get axis label for minorLogTicks	getAxisLabel
get color ramp by name, color, or function	getColorRamp
get simple date string	getDate
Get aspect ratio for coordinates, plot, or device	getPlotAspect
Search for objects in the environment	grepls
Draw grouped axis labels	groupedAxis
Global substitution into ordered factor	gsubOrdered
Pattern replacement with multiple patterns	gsubs
Handle function arguments as text	handleArgsText
convert HCL to R color	hcl2col
Apply head() across each element in a list of vectors	heads
Return Heatmap column order from ComplexHeatmap heatmap object	heatmap_column_order
Return Heatmap row order from ComplexHeatmap heatmap object	heatmap_row_order
convert HCL to R color	hsl2col
Convert HSV matrix to R color	hsv2col
case-insensitive grep	igrep
vector contains any case-insensitive grep match	igrepHas
case-insensitive logical grepl	igrepl
Display color raster image using a matrix of colors	imageByColors
Display a color raster image	imageDefault
detect valid R color	isColor
Vectorized isFALSE	isFALSEV
Vectorized isTRUE	isTRUEV
Jam-specific recursive apply	jam_rapply
Calculate scatter plot point density	jamCalcDensity
Show R function arguments jam-style	jargs
Extend kableExtra colorization of 'Rmarkdown' tables	kable_coloring
Convert list of vectors to data.frame with item, value, name	list2df
Long listing of R session objects	lldf
log2 transformation with directionality	log2signed
vectorized make_styles for html span output	make_html_styles
vectorized make_styles for crayon output	make_styles
make R colors darker (or lighter)	makeColorDarker
make unique vector names	makeNames
Merge list of data.frames retaining all rows	mergeAllXY
Return the middle portion of data similar to head and tail	middle
Calculate major and minor tick marks for log-scale axis	minorLogTicks
Display major and minor tick marks for log-scale axis	logFoldAxis minorLogTicksAxis pvalueAxis
order alphanumeric values keeping numeric values in proper order	mixedOrder
sort alphanumeric values keeping numeric values in proper order	mixedSort
sort data.frame keeping numeric values in proper order	mixedSortDF
sort alphanumeric values within a list format	mixedSorts
order alphanumeric values from a list	mmixedOrder
assign unique names for a vector	nameVector
define a named vector using vector names	nameVectorN
Return the newest file from a vector of files	newestFile
Apply noise floor and ceiling to numeric vector	noiseFloor
Scale a numeric vector from 0 to 1	normScale
Create a blank plot with optional labels	nullPlot
prefix integers with leading zeros	padInteger
pad a character string to a fixed length	padString
Paste data.frame rows into character vector	pasteByRow
Paste data.frame rows into an ordered factor	pasteByRowOrdered
Plot distribution and histogram overlay	plotPolygonDensity
Plot ridges density plots for numeric matrix input	plotRidges
Smooth scatter plot with enhancements	plotSmoothScatter
print colorized output to R console	printDebug printDebugHtml printDebugI
provigrep: progressive case-insensitive value-grep	proigrep provigrep
Convert radians to degrees	rad2deg
Simple rainbow palette replacement	rainbow2
rbind a list of vectors into matrix or data.frame	rbindList
Import one or more data.frame from 'Excel' 'xlsx' format	readOpenxlsx
relist a vector which allows re-ordered names	relist_named
Reload 'Rmarkdown' cache	reload_rmarkdown_cache
Rename columns in a data.frame, matrix, tibble, or GRanges object	renameColumn
Convert RGB color matrix to R color	rgb2col
lengths for recursive lists	rlengths
remove Infinite values	rmInfinite
remove NA values	rmNA
remove NA values from list elements	rmNAs
remove NULL entries from list	rmNULL
Calculate row group means, or other statistics	rowGroupMeans rowGroupRmOutliers
Remove outlier points per row by MAD factor threshold	rowRmMadOutliers
return the classes of a list of objects	sclass
print dimensions of list object elements	sdim sdima ssdim ssdima
Set column widths in Xlsx files	set_xlsx_colwidths
Set row heights in Xlsx files	set_xlsx_rowheights
Get Chroma and Luminance ranges for the given lightMode	setCLranges
set R prompt with project name and R version	setPrompt
Define visible text color	setTextContrastColor
Draw text with shadow border	shadowText
Get and set options for shadowText	shadowText_options
Show colors from a vector or list	showColors
convert size to numeric value	sizeAsNum
Smooth scatter plot, Jam style	smoothScatterJam
Determine square root axis tick mark positions	sqrtAxis
frequency of entries, ordered by frequency	tcount
Uppercase the first letter in each word	ucfirst
Remove alpha transparency from colors	unalpha
case-insensitive grep, returning unmatched indices	unigrep
apply unique to each element of a list	uniques
Un-nest a nested list into a simple list	unnestList
case-insensitive grep, returning unmatched values	unvigrep
Draw colored box indicating R plot space	usrBox
grep, returning values	vgrep
case-insensitive grep, returning values	vigrep
Warp a vector of numeric values relative to zero	warpAroundZero
Warp colors in a color ramp	warpRamp
Export a data.frame to 'Excel' 'xlsx' format	writeOpenxlsx