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 | |
| No Results! | ||
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 | ||
| No Results! | ||
Last month downloads
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 |
| suggests | Cairo (>= 1.5-1) , knitr |
| depends | cluster (>= 1.14.4) , grid , hexbin (>= 1.26.3) , lattice (>= 0.20-27) , latticeExtra (>= 0.6-26) , R (>= 3.0.2) |
| imports | e1071 , gridExtra , gtable , MASS (>= 7.3-29) , tools |
| Contributors | the R Core Team, Robert Gentleman, Ross Ihaka, The R Foundation, Jennifer Aguiar , Ontario Institute for Cancer Research |
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