Functions to Create Publication-Quality Plots


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Documentation for package ‘BoutrosLab.plotting.general’ version 6.0.3

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BoutrosLab.plotting.general-package Boutros Lab general plotting functions
auto.axis Create ideal labels and values for a given dataset (detects log scales)
BoutrosLab.plotting.general Boutros Lab general plotting functions
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
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
ks.test.critical.value Critical Value for Kolmogorov-Smirnov Test
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