Functions to Create Publication-Quality Plots

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Documentation for package ‘BoutrosLab.plotting.general’ version 7.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

auto.axis	Create ideal labels and values for a given numeric vector (detects log scales)
CNA	Copy number aberration (CNA) data from colon cancer patients
color.gradient	Creates a colour gradient
colour.gradient	Creates a colour gradient
covariates.grob	Create one or more covariate bars
create.barplot	Make a barplot
create.boxplot	Make a boxplot
create.colorkey	Create Colourkey
create.colourkey	Create Colourkey
create.dendrogram	Generate a dendrogram
create.densityplot	Make a density plot
create.dotmap	Make a dotmap with coloured background
create.gif	Make a gif
create.heatmap	Make a heatmap
create.hexbinplot	Make a hexagonally binned plot
create.histogram	Make a histogram
create.lollipopplot	Make a lollipopplot
create.manhattanplot	Make a Manhattan plot
create.multipanelplot	Joins plots together
create.multiplot	Joins plots together
create.polygonplot	Make a polygonplot
create.qqplot.comparison	Make a quantile-quantile plot of two samples
create.qqplot.fit	Make a quantile-quantile plot of a sample
create.qqplot.fit.confidence.interval	Create the confidence bands for a one-sample qq plot
create.scatterplot	Make a scatterplot
create.segplot	Make a segplot
create.stripplot	Make a strip-plot
create.violinplot	Make a violin plot
critical.value.ks.test	Critical Value for Kolmogorov-Smirnov Test
default.colors	Provides default colour schemes.
default.colours	Provides default colour schemes.
display.colors	Function to display R colors, as well as corresponding R grey colours.
display.colours	Function to display R colors, as well as corresponding R grey colours.
display.statistical.result	Utility function to display statistical result in a plot
dist	Distance Matrix Computation
force.color.scheme	Based on predefined colour schemes, returns a vector of corresponding colours.
force.colour.scheme	Based on predefined colour schemes, returns a vector of corresponding colours.
generate.at.final	Generates alternative default tick mark locations for create.densityplot() and create.scatterplot()
get.corr.key	Correlation Key
get.correlation.p.and.corr	Calculate a correlation and its statistical significance
get.defaults	Get operating system specific default properties
get.line.breaks	Get line breaks
legend.grob	Generate a legend grob
microarray	Microarray dataset of colon cancer patients
panel.BL.bwplot	A lattice::panel.bwplot replacement that fixes colouring issues
patient	Dataset describing qualities of 58 colon cancer patients
pcawg.colors	Return standard PCAWG colour palettes.
pcawg.colours	Return standard PCAWG colour palettes.
scientific.notation	Use scientific notation in plots
show.available.palettes	Display the available colour palettes
SNV	Single nucleotide variant (SNV) data from colon cancer patients
thousands.split	Divide strings into groups of thousands
write.metadata	Writes Metadata
write.plot	Simplifies plotting by standardizing and centralizing all output-handling