Package: jamba 1.0.2

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
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jamba.pdf |jamba.html
jamba/json (API)
NEWS

# Install 'jamba' in R:
install.packages('jamba', repos = c('https://jmw86069.r-universe.dev', 'https://cloud.r-project.org'))

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

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

On CRAN:

Conda:

bioinformatics

5.43 score 6 stars 143 exports 4 dependencies

Last updated 9 days agofrom:6408d12350. Checks:7 OK, 2 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 11 2025
R-4.5-winOKMar 11 2025
R-4.5-macOKMar 11 2025
R-4.5-linuxOKMar 11 2025
R-4.4-winOKMar 11 2025
R-4.4-macOKMar 11 2025
R-4.4-linuxOKMar 11 2025
R-4.3-winNOTEMar 11 2025
R-4.3-macNOTEMar 11 2025

Exports:adjustAxisLabelMarginsalpha2colapplyCLrangeapplyXlsxCategoricalFormatapplyXlsxConditionalFormatasDateasSizebreakDensitybreaksByVectorcall_fn_ellipsiscell_fun_labelcheck_pkg_installedcheckLightModecol2alphacol2hclcol2hslcol2hsvcolNum2excelNamecolor_dithercolor2gradientcoordPresetscPastecPasteScPasteSUcPasteUcPasteUniquedateToDaysOlddecideMfrowdeg2raddrawLabelsexp2signedfillBlanksfixYellowfixYellowHueformatIntgetAxisLabelgetColorRampgetDategetPlotAspectgreplsgroupedAxisgsubOrderedgsubshandleArgsTexthcl2colheadsheatmap_column_orderheatmap_row_orderhsl2colhsv2coligrepigrepHasigreplimageByColorsimageDefaultisColorisFALSEVisTRUEVjam_rapplyjamCalcDensityjargskable_coloringlist2dflldflog2signedlogFoldAxismake_html_stylesmake_stylesmakeColorDarkermakeNamesmergeAllXYmiddleminorLogTicksminorLogTicksAxismixedOrdermixedSortmixedSortDFmixedSortsmmixedOrdernameVectornameVectorNnewestFilenoiseFloornormScalenullPlotpadIntegerpadStringpasteByRowpasteByRowOrderedplotPolygonDensityplotRidgesplotSmoothScatterprintDebugprintDebugHtmlprintDebugIproigrepprovigreppvalueAxisrad2degrainbow2rbindListreadOpenxlsxrelist_namedreload_rmarkdown_cacherenameColumnrgb2colrlengthsrmInfinitermNArmNAsrmNULLrowGroupMeansrowGroupRmOutliersrowRmMadOutlierssclasssdimsdimaset_xlsx_colwidthsset_xlsx_rowheightssetCLrangessetPromptsetTextContrastColorshadowTextshadowText_optionsshowColorssizeAsNumsmoothScatterJamsqrtAxisssdimssdimatcountucfirstunalphaunigrepuniquesunnestListunvigrepusrBoxvgrepvigrepwarpAroundZerowarpRampwriteOpenxlsx

Dependencies:colorspaceKernSmoothRColorBrewerwithr

Jamba Overview

Rendered fromjamba-vignette.Rmdusingknitr::rmarkdownon Mar 11 2025.

Last update: 2025-03-04
Started: 2017-08-31

Readme and manuals

Help Manual

Help pageTopics
Adjust axis label marginsadjustAxisLabelMargins
set R color alpha valuealpha2col
Apply CL color rangeapplyCLrange
Add categorical colors to 'Excel' 'xlsx' worksheetsapplyXlsxCategoricalFormat
Xlsx Conditional formattingapplyXlsxConditionalFormat
convert date DDmmmYYYY to DateasDate
convert numeric value or R object to human-readable sizeasSize
Calculate more detailed density of numeric valuesbreakDensity
break a vector into groupsbreaksByVector
Safely call a function using ellipsiscall_fn_ellipsis
ComplexHeatmap cell function to label heatmap cellscell_fun_label
Lightweight method to check if an R package is installedcheck_pkg_installed
check lightMode for light background colorcheckLightMode
get R color alpha valuecol2alpha
convert R color to HCL color matrixcol2hcl
convert R color to HSL color matrixcol2hsl
Convert R color to HSV matrixcol2hsv
convert column number to 'Excel' column namecolNum2excelName
Make dithered color pattern light-darkcolor_dither
Make a color gradientcolor2gradient
Process coordinate adjustment presetscoordPresets
paste a list into a delimited vectorcPaste cPasteS cPasteSU cPasteU cPasteUnique
convert date to age in daysdateToDaysOld
Decide plot panel rows, columns for graphics::par(mfrow)decideMfrow
Convert degrees to radiansdeg2rad
Draw text labels on a base R plotdrawLabels
exponentiate log2 values with directionalityexp2signed
Fill blank entries in a vectorfillBlanks
Fix yellow colorfixYellow
Fix yellow color huefixYellowHue
Format an integer as a stringformatInt
Get axis label for minorLogTicksgetAxisLabel
get color ramp by name, color, or functiongetColorRamp
get simple date stringgetDate
Get aspect ratio for coordinates, plot, or devicegetPlotAspect
Search for objects in the environmentgrepls
Draw grouped axis labelsgroupedAxis
Global substitution into ordered factorgsubOrdered
Pattern replacement with multiple patternsgsubs
Handle function arguments as texthandleArgsText
convert HCL to R colorhcl2col
Apply head() across each element in a list of vectorsheads
Return Heatmap column order from ComplexHeatmap heatmap objectheatmap_column_order
Return Heatmap row order from ComplexHeatmap heatmap objectheatmap_row_order
convert HCL to R colorhsl2col
Convert HSV matrix to R colorhsv2col
case-insensitive grepigrep
vector contains any case-insensitive grep matchigrepHas
case-insensitive logical grepligrepl
Display color raster image using a matrix of colorsimageByColors
Display a color raster imageimageDefault
detect valid R colorisColor
Vectorized isFALSEisFALSEV
Vectorized isTRUEisTRUEV
Jam-specific recursive applyjam_rapply
Calculate scatter plot point densityjamCalcDensity
Show R function arguments jam-stylejargs
Extend kableExtra colorization of 'Rmarkdown' tableskable_coloring
Convert list of vectors to data.frame with item, value, namelist2df
Long listing of R session objectslldf
log2 transformation with directionalitylog2signed
vectorized make_styles for html span outputmake_html_styles
vectorized make_styles for crayon outputmake_styles
make R colors darker (or lighter)makeColorDarker
make unique vector namesmakeNames
Merge list of data.frames retaining all rowsmergeAllXY
Return the middle portion of data similar to head and tailmiddle
Calculate major and minor tick marks for log-scale axisminorLogTicks
Display major and minor tick marks for log-scale axislogFoldAxis minorLogTicksAxis pvalueAxis
order alphanumeric values keeping numeric values in proper ordermixedOrder
sort alphanumeric values keeping numeric values in proper ordermixedSort
sort data.frame keeping numeric values in proper ordermixedSortDF
sort alphanumeric values within a list formatmixedSorts
order alphanumeric values from a listmmixedOrder
assign unique names for a vectornameVector
define a named vector using vector namesnameVectorN
Return the newest file from a vector of filesnewestFile
Apply noise floor and ceiling to numeric vectornoiseFloor
Scale a numeric vector from 0 to 1normScale
Create a blank plot with optional labelsnullPlot
prefix integers with leading zerospadInteger
pad a character string to a fixed lengthpadString
Paste data.frame rows into character vectorpasteByRow
Paste data.frame rows into an ordered factorpasteByRowOrdered
Plot distribution and histogram overlayplotPolygonDensity
Plot ridges density plots for numeric matrix inputplotRidges
Smooth scatter plot with enhancementsplotSmoothScatter
print colorized output to R consoleprintDebug printDebugHtml printDebugI
provigrep: progressive case-insensitive value-grepproigrep provigrep
Convert radians to degreesrad2deg
Simple rainbow palette replacementrainbow2
rbind a list of vectors into matrix or data.framerbindList
Import one or more data.frame from 'Excel' 'xlsx' formatreadOpenxlsx
relist a vector which allows re-ordered namesrelist_named
Reload 'Rmarkdown' cachereload_rmarkdown_cache
Rename columns in a data.frame, matrix, tibble, or GRanges objectrenameColumn
Convert RGB color matrix to R colorrgb2col
lengths for recursive listsrlengths
remove Infinite valuesrmInfinite
remove NA valuesrmNA
remove NA values from list elementsrmNAs
remove NULL entries from listrmNULL
Calculate row group means, or other statisticsrowGroupMeans rowGroupRmOutliers
Remove outlier points per row by MAD factor thresholdrowRmMadOutliers
return the classes of a list of objectssclass
print dimensions of list object elementssdim sdima ssdim ssdima
Set column widths in Xlsx filesset_xlsx_colwidths
Set row heights in Xlsx filesset_xlsx_rowheights
Get Chroma and Luminance ranges for the given lightModesetCLranges
set R prompt with project name and R versionsetPrompt
Define visible text colorsetTextContrastColor
Draw text with shadow bordershadowText
Get and set options for shadowTextshadowText_options
Show colors from a vector or listshowColors
convert size to numeric valuesizeAsNum
Smooth scatter plot, Jam stylesmoothScatterJam
Determine square root axis tick mark positionssqrtAxis
frequency of entries, ordered by frequencytcount
Uppercase the first letter in each worducfirst
Remove alpha transparency from colorsunalpha
case-insensitive grep, returning unmatched indicesunigrep
apply unique to each element of a listuniques
Un-nest a nested list into a simple listunnestList
case-insensitive grep, returning unmatched valuesunvigrep
Draw colored box indicating R plot spaceusrBox
grep, returning valuesvgrep
case-insensitive grep, returning valuesvigrep
Warp a vector of numeric values relative to zerowarpAroundZero
Warp colors in a color rampwarpRamp
Export a data.frame to 'Excel' 'xlsx' formatwriteOpenxlsx