Gplots Heatmap
Heatmap.2 (gplots) how to change horizontal size of the color key and add a legend. Constraints and margins in xcode 6, margins revealing whitespace after snap. R gplots: Heatmap with side colours. R - heatmap.2 (gplots): change colors for breaks. Available stack size is not used by R, returning “Error: node stack overflow”. This articles describes how to create and customize an interactive heatmap in R using the heatmaply R package, which is based on the ggplot2 and plotly.js engine. Most basic heatmap with ggplot2 This is the most basic heatmap you can build with R and ggplot2, using the geomtile function. Input data must be a long format where each row provides an observation. At least 3 variables are needed per observation. Enhanced heatmap representation with partition and summary statistics (optional). This is an enhanced version of `heatmap.2' function in the Package gplots. The enhancement includes: 1) Improved performance with optional input of precomputed dist object and hclust object. 2) Highlight of specific cells using rectangles.
Various R Programming Tools for Plotting Data
Various R programming tools for plotting data, including:- calculating and plotting locally smoothed summary function as('bandplot', 'wapply'),- enhanced versions of standard plots ('barplot2', 'boxplot2','heatmap.2', 'smartlegend'),- manipulating colors ('col2hex', 'colorpanel', 'redgreen','greenred', 'bluered', 'redblue', 'rich.colors'),- calculating and plotting two-dimensional data summaries ('ci2d','hist2d'),- enhanced regression diagnostic plots ('lmplot2', 'residplot'),- formula-enabled interface to 'stats::lowess' function ('lowess'),- displaying textual data in plots ('textplot', 'sinkplot'),- plotting a matrix where each cell contains a dot whose sizereflects the relative magnitude of the elements ('balloonplot'),- plotting 'Venn' diagrams ('venn'),- displaying Open-Office style plots ('ooplot'),- plotting multiple data on same region, with separate axes('overplot'),- plotting means and confidence intervals ('plotCI', 'plotmeans'),- spacing points in an x-y plot so they don't overlap ('space').
Readme
Introduction
This repo is to keep the gplots package alive. I don't plan to develop new features, but if you'll send pull requests I'm willing to review them.
Latest news
You can see the most recent changes to the package in the NEWS.md file
Code of conduct
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
Installation
To install the stable version on CRAN:
And then you may load the package using:
Usage
TODO
Contact
You are welcome to:
- Ask questions on: https://stackoverflow.com/questions/tagged/gplots
- Submit suggestions and bug-reports at: https://github.com/talgalili/gplots/issues
- Send a pull request on: https://github.com/talgalili/gplots/
- Compose a friendly e-mail to: tal.galili@gmail.com
R Gplots Heatmap.2
Functions in gplots
| Name | Description | |
| barplot2 | Enhanced Bar Plots | |
| bandplot | Plot x-y Points with Locally Smoothed Mean and Standard Deviation | |
| balloonplot | Plot a graphical matrix where each cell contains a dot whose size reflects the relative magnitude of the corresponding component. | |
| angleAxis | Add a Axis to a Plot with Rotated Labels | |
| colorpanel | Generate a smoothly varying set of colors | |
| col2hex | Convert color names to hex RGB strings | |
| boxplot2 | Produce a Boxplot Annotated with the Number of Observations | |
| gplots-defunct | Defunct functions | |
| gplots-deprecated | Deprecated functions | |
| ci2d | Create 2-dimensional empirical confidence regions | |
| plotCI | Plot Error Bars and Confidence Intervals | |
| plotmeans | Plot Group Means and Confidence Intervals | |
| reorder.factor | Reorder the Levels of a Factor | |
| ooplot.default | Create an OpenOffice style plot | |
| overplot | Plot multiple variables on the same region, with appropriate axes | |
| qqnorm.aov | Makes a half or full normal plot for the effects from an aov model | |
| textplot | Display text information in a graphics plot. | |
| rtPCR | Teratogenesis rtPCR data | |
| rich.colors | Rich Color Palettes | |
| space | Space points in an x-y plot so they don't overlap. | |
| heatmap.2 | Enhanced Heat Map | |
| lmplot2 | Plots to assess the goodness of fit for the linear model objects | |
| hist2d | Compute and Plot a 2-Dimensional Histogram | |
| residplot | Undocumented functions | |
| venn | Plot a Venn diagram | |
| wapply | Compute the Value of a Function Over a Local Region Of An X-Y Plot | |
| lowess | Scatter Plot Smoothing | |
| sinkplot | Send textual R output to a graphics device | |
| No Results! | ||
Vignettes of gplots
Gplots Heatmap Example
| Name | ||
| venn.Rnw | ||
| No Results! | ||
Last month downloads
Details
Plots Heatmap
| VignetteBuilder | knitr |
| Date | 2020-11-28 |
| License | GPL-2 |
| URL | https://github.com/talgalili/gplots |
| BugReports | https://github.com/talgalili/gplots/issues |
| NeedsCompilation | no |
| Packaged | 2020-11-28 13:04:00 UTC; talgalili |
| Repository | CRAN |
| Date/Publication | 2020-11-28 13:50:02 UTC |
| imports | caTools , gtools , KernSmooth , stats |
| suggests | grid , knitr , MASS |
| depends | R (>= 3.0) |
| Contributors | Steffen Moeller, Bill Venables, Ben Bolker, Thomas Lumley, Marc Schwartz, Lodewijk Bonebakker, Andy Liaw, Arni Magnusson, Robert Gentleman, Martin Maechler, Gregory R. Warnes, Wolfgang Huber |
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Gplots Heatmap.2
[](http://www.rdocumentation.org/packages/gplots)