Package: colorpatch 0.1.2

colorpatch: Optimized Rendering of Fold Changes and Confidence Values

Shows color patches for encoding fold changes (e.g. log ratios) together with confidence values within a single diagram. This is especially useful for rendering gene expression data as well as other types of differential experiments. In addition to different rendering methods (ggplot extensions) functionality for perceptually optimizing color palettes are provided. Furthermore the package provides extension methods of the colorspace color-class in order to simplify the work with palettes (a.o. length, as.list, and append are supported).

Authors:Andre Mueller [aut, cre], Hans Kestler [aut]

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colorpatch.pdf |colorpatch.html✨
colorpatch/json (API)
NEWS

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

Peer review:

Datasets:
  • GreenRedRGB - Standard RGB Green/Red two-sided color scale.
  • OptimBlueYellowLAB - Optimum RGB Blue/Yellow two-sided color scale in LAB color space.
  • OptimGreenRedLAB - Optimum RGB Green/Red two-sided color scale in LAB color space.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.23 score 34 scripts 477 downloads 30 exports 33 dependencies

Last updated 7 years agofrom:27edcc0586. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winNOTENov 01 2024
R-4.5-linuxNOTENov 01 2024
R-4.4-winNOTENov 01 2024
R-4.4-macNOTENov 01 2024
R-4.3-winNOTENov 01 2024
R-4.3-macNOTENov 01 2024

Exports:appendapply.coloras.listColorDistanceColorPatchColorFunColorPatchSizeFunColorRgbFunComputeSymmetryCreateClusteredDataCreateExampleDataDistColorDistColorFunFindUniformSequenceGeneratePalettesHsvColorFunHsvSizeFunInterpolateColorFunLinColorSpaceOptimizeBiColorOrderDataOrderDataHclustOrderDataTSPOrderWithTSPPlotSymmetryPlotUniformityReadArraySRGBstat_bicolorstat_colorpatchtheme_colorpatchToDataFrame

Dependencies:clicodetoolscolorspacefansifarverforeachggplot2gluegridExtragtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleTSPutf8vctrsviridisLitewithr

colorpatch Package Introduction

André Müller

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2017-06-10
Started: 2017-06-10

Readme and manuals

Help Manual

Help pageTopics
A small introduction to the colorpatch package.colorpatch-package colorpatch
Appends two palettes to form a single palette.append,color-method
Applies a function to each entry of a colorspace::color palette.apply.color
Transforms palette to list of single colors.as
Creates a list with single colors from a palette.as.list as.list,color-method
Computes the perceptional distance between two neighboring colorsColorDistance
Creates a color function mapping (ratio, conf) tuples to a single colorColorPatchColorFun
Creates a size function mapping (ratio, conf) to a single colorColorPatchSizeFun
Creates a color mapping functionColorRgbFun
Computes the symmetry of a given bi-variate color paletteComputeSymmetry
Creates clustered random dataCreateClusteredData
Creates demonstration data of the colorpatch packageCreateExampleData
Computes the distance of to colors within a certain colorspaceDistColor
Creates a color distance functionDistColorFun
Finds a uniform color sequence within a non-uniform palette by subsampling that paletteFindUniformSequence
Creates color palettes and saves them as filesGeneratePalettes
Standard RGB Green/Red two-sided color scale.GreenRedRGB
Creates a color function mapping ratio/conf values to a HSV colorspaceHsvColorFun
Creates a size function mapping ratio/conf to a patch size for bicoloringsHsvSizeFun
Linear interpolation within a colorspace::color paletteInterpolateColorFun
Returns the length of a palette (the number of entries).length,color-method
Creates a linear color space between two colorsLinColorSpace
Optimum RGB Blue/Yellow two-sided color scale in LAB color space.OptimBlueYellowLAB
Optimum RGB Green/Red two-sided color scale in LAB color space.OptimGreenRedLAB
Optimizes a bicolor paletteOptimizeBiColor
Orders rows and columns of data.OrderData
Orders rows and column distances with 'stats::hclust()'OrderDataHclust
Orders rows and column distances with traveling salesman ordering TSPOrderDataTSP
Orders a data set given a distance matrix with TSPOrderWithTSP
Plots the symmetry of a bivariate color scalePlotSymmetry
Plots the uniformity of a color palettePlotUniformity
Reads a sRGB color table as CSV fileReadArraySRGB
Plots a ratio/confidence plot using a bivariate colormapstat_bicolor
A stat function for the use with ggplot2stat_colorpatch
A ggplot2::ggproto class for showing color patches.StatColorPatch
A ggplot2 theme for rendering colorpatches (black background)theme_colorpatch
Transforms a ratio/conf data set to a ggplot dataframeToDataFrame