# Functions to Create Publication-Quality Plots

## Documentation for package ‘BoutrosLab.plotting.general’ version 5.3.4

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

## Help Pages

BoutrosLab.plotting.general-package | Boutros Lab general plotting functions
append.footnote | Appends Footnotes to Grid Objects
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.heatmap | Make a heatmap
create.hexbinplot | Make a hexagonally binned plot
create.histogram | Make a histogram
create.manhattanplot | Make a Manhattan plot
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.
GarbageCollect | Force Garbage Collection
generate.at.final | Generates alternative default tick mark locations for create.densityplot() and create.scatterplot()
generate.filename | Generate a filename in the lab standard
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
ls.objects | List of objects
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
recode.vector | Recode Vector
save.session.profile | Save Session Profile
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
write.metadata | Writes Metadata
write.plot | Simplifies plotting by standardizing and centralizing all output-handling