BoutrosLab.plotting.general v5.9.2

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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.

Functions in BoutrosLab.plotting.general

Name Description
GarbageCollect 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 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.segplot Make a segplot
create.scatterplot Make a scatterplot
get.line.breaks Get line breaks
panel.BL.bwplot A lattice::panel.bwplot replacement that fixes colouring issues
create.gif Make a gif
write.plot 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
get.corr.key Correlation Key
create.stripplot Make a strip-plot
create.densityplot Make a density plot
create.violinplot Make a violin plot
create.dotmap Make a dotmap with coloured background
SNV 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.heatmap Make a heatmap
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
dist Distance Matrix Computation
scientific.notation Use scientific notation in plots
ls.objects List of objects
legend.grob 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.defaults Get operating system specific default properties
patient Dataset describing qualities of 58 colon cancer patients
recode.vector Recode Vector
save.session.profile Save Session Profile
thousands.split Divide strings into groups of thousands
pcawg.colours 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.
write.metadata Writes Metadata
covariates.grob Create one or more covariate bars
colour.gradient Creates a colour gradient
CNA 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
auto.axis Create ideal labels and values for a given dataset (detects log scales)
create.boxplot Make a boxplot
create.barplot Make a barplot
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Vignettes of BoutrosLab.plotting.general

Name
Figures/Multiplot_Ex2.png
Figures/chart-types.png
Figures/colour_wheel.png
Figures/ex2_schematic.pdf
Figures/intro_plotting_ex.png
PlottingGuide.Rnw
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Details

Type Package
Date 2018-04-10
License GPL-2
LazyLoad yes
LazyData yes
VignetteBuilder knitr
NeedsCompilation yes
Packaged 2018-04-20 18:35:31 UTC; jgreen
Repository CRAN
Date/Publication 2018-04-23 08:33:00 UTC

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