Package: BoutrosLab.plotting.general 7.1.2

Paul Boutros

BoutrosLab.plotting.general: Functions to Create Publication-Quality Plots

Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi:10.1186/s12859-019-2610-2>.

Authors:Paul Boutros [aut, cre], Christine P'ng [ctb], Jeff Green [ctb], Stephenie Prokopec [ctb], Ontario Institute for Cancer Research [cph], The R Core Team [cph], The R Foundation [cph], Robert Gentleman [ctb], Ross Ihaka [ctb], Caden Bugh [ctb], Dan Knight [ctb], Stefan Eng [ctb], Mohammed Faizal Eeman Mootor [ctb], Rachel Dang [ctb], John Sahrmann [ctb]

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BoutrosLab.plotting.general.pdf |BoutrosLab.plotting.general.html✨
BoutrosLab.plotting.general/json (API)
NEWS

# Install 'BoutrosLab.plotting.general' in R:
install.packages('BoutrosLab.plotting.general', repos = c('https://uclahs-cds.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/uclahs-cds/package-boutroslab-plotting-general/issues

Datasets:
  • CNA - Copy number aberration (CNA) data from colon cancer patients
  • SNV - Single nucleotide variant (SNV) data from colon cancer patients
  • microarray - Microarray dataset of colon cancer patients
  • patient - Dataset describing qualities of 58 colon cancer patients

On CRAN:

43 exports 11 stars 3.18 score 21 dependencies 6 dependents 233 scripts 527 downloads

Last updated 3 months agofrom:54fb8b7afc. Checks:ERROR: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesFAILAug 29 2024
R-4.5-win-x86_64WARNINGAug 29 2024
R-4.5-linux-x86_64WARNINGAug 29 2024
R-4.4-win-x86_64WARNINGAug 29 2024
R-4.4-mac-x86_64WARNINGAug 29 2024
R-4.4-mac-aarch64WARNINGAug 29 2024
R-4.3-win-x86_64WARNINGAug 29 2024
R-4.3-mac-x86_64WARNINGAug 29 2024
R-4.3-mac-aarch64WARNINGAug 29 2024

Exports:auto.axiscolour.gradientcovariates.grobcreate.barplotcreate.boxplotcreate.colourkeycreate.dendrogramcreate.densityplotcreate.dotmapcreate.gifcreate.heatmapcreate.hexbinplotcreate.histogramcreate.lollipopplotcreate.manhattanplotcreate.multipanelplotcreate.multiplotcreate.polygonplotcreate.qqplot.comparisoncreate.qqplot.fitcreate.qqplot.fit.confidence.intervalcreate.scatterplotcreate.segplotcreate.stripplotcreate.violinplotcritical.value.ks.testdefault.coloursdisplay.coloursdisplay.statistical.resultdistforce.colour.schemegenerate.at.finalget.corr.keyget.correlation.p.and.corrget.defaultsget.line.breakslegend.grobpcawg.coloursscientific.notationshow.available.palettesthousands.splitwrite.metadatawrite.plot

Dependencies:classcliclusterdeldire1071gluegridExtragtablehexbininterpjpeglatticelatticeExtralifecycleMASSpngproxyRColorBrewerRcppRcppEigenrlang

Readme and manuals

Help Manual

Help pageTopics
Create ideal labels and values for a given numeric vector (detects log scales)auto.axis
Copy number aberration (CNA) data from colon cancer patientsCNA
Creates a colour gradientcolor.gradient colour.gradient
Create one or more covariate barscovariates.grob
Make a barplotcreate.barplot
Make a boxplotcreate.boxplot
Create Colourkeycreate.colorkey create.colourkey
Generate a dendrogramcreate.dendrogram
Make a density plotcreate.densityplot
Make a dotmap with coloured backgroundcreate.dotmap
Make a gifcreate.gif
Make a heatmapcreate.heatmap
Make a hexagonally binned plotcreate.hexbinplot
Make a histogramcreate.histogram
Make a lollipopplotcreate.lollipopplot
Make a Manhattan plotcreate.manhattanplot
Joins plots togethercreate.multipanelplot
Joins plots togethercreate.multiplot
Make a polygonplotcreate.polygonplot
Make a quantile-quantile plot of two samplescreate.qqplot.comparison
Make a quantile-quantile plot of a samplecreate.qqplot.fit
Create the confidence bands for a one-sample qq plotcreate.qqplot.fit.confidence.interval
Make a scatterplotcreate.scatterplot
Make a segplotcreate.segplot
Make a strip-plotcreate.stripplot
Make a violin plotcreate.violinplot
Critical Value for Kolmogorov-Smirnov Testcritical.value.ks.test
Provides default colour schemes.default.colors default.colours
Function to display R colors, as well as corresponding R grey colours.display.colors display.colours
Utility function to display statistical result in a plotdisplay.statistical.result
Distance Matrix Computationdist
Based on predefined colour schemes, returns a vector of corresponding colours.force.color.scheme force.colour.scheme
Generates alternative default tick mark locations for create.densityplot() and create.scatterplot()generate.at.final
Correlation Keyget.corr.key
Calculate a correlation and its statistical significanceget.correlation.p.and.corr
Get operating system specific default propertiesget.defaults
Get line breaksget.line.breaks
Generate a legend groblegend.grob
Microarray dataset of colon cancer patientsmicroarray
A lattice::panel.bwplot replacement that fixes colouring issuespanel.BL.bwplot
Dataset describing qualities of 58 colon cancer patientspatient
Return standard PCAWG colour palettes.pcawg.colors pcawg.colours
Use scientific notation in plotsscientific.notation
Display the available colour palettesshow.available.palettes
Single nucleotide variant (SNV) data from colon cancer patientsSNV
Divide strings into groups of thousandsthousands.split
Writes Metadatawrite.metadata
Simplifies plotting by standardizing and centralizing all output-handlingwrite.plot