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BoutrosLab.plotting.general (version 5.9.2)

Create Publication-Quality Plots

Description

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.

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Version

Install

install.packages('BoutrosLab.plotting.general')

Monthly Downloads

553

Version

5.9.2

License

GPL-2

Maintainer

Paul Boutros

Last Published

April 23rd, 2018

Functions in BoutrosLab.plotting.general (5.9.2)

Force Garbage Collection

force.colour.scheme

Based on predefined colour schemes, returns a vector of corresponding colours.

create.hexbinplot

Make a hexagonally binned plot

Microarray dataset of colon cancer patients

generate.at.final

Generates alternative default tick mark locations for create.densityplot() and create.scatterplot()

create.histogram

Make a histogram

create.lollipopplot

Make a lollipopplot

create.scatterplot

Make a scatterplot

get.line.breaks

Get line breaks

panel.BL.bwplot

A lattice::panel.bwplot replacement that fixes colouring issues

Simplifies plotting by standardizing and centralizing all output-handling

generate.filename

Generate a filename in the lab standard

ks.test.critical.value

Critical Value for Kolmogorov-Smirnov Test

Correlation Key

create.stripplot

Make a strip-plot

create.densityplot

Make a density plot

create.violinplot

Make a violin plot

Make a dotmap with coloured background

Single nucleotide variant (SNV) data from colon cancer patients

create.colourkey

Create Colourkey

create.dendrogram

Generate a dendrogram

create.manhattanplot

Make a Manhattan plot

create.qqplot.fit

Make a quantile-quantile plot of a sample

create.polygonplot

Make a polygonplot

create.qqplot.fit.confidence.interval

Create the confidence bands for a one-sample qq plot

display.statistical.result

Utility function to display statistical result in a plot

create.multipanelplot

Joins plots together

get.correlation.p.and.corr

Calculate a correlation and its statistical significance

Distance Matrix Computation

scientific.notation

Use scientific notation in plots

List of objects

Generate a legend grob

create.multiplot

Joins plots together

show.available.palettes

Display the available colour palettes

create.qqplot.comparison

Make a quantile-quantile plot of two samples

Get operating system specific default properties

Dataset describing qualities of 58 colon cancer patients

save.session.profile

Save Session Profile

thousands.split

Divide strings into groups of thousands

Return standard PCAWG colour palettes.

display.colours

Function to display R colors, as well as corresponding R grey colours.

default.colours

Provides default colour schemes.

Writes Metadata

covariates.grob

Create one or more covariate bars

colour.gradient

Creates a colour gradient

Copy number aberration (CNA) data from colon cancer patients

BoutrosLab.plotting.general-package

Boutros Lab general plotting functions

append.footnote

Appends Footnotes to Grid Objects

Create ideal labels and values for a given dataset (detects log scales)