Table of Contents
- Base
- Tutorial
- Packages
- Text
- Performance
- Data wrangling
- CLI
- ML
- Visualization
- Color
- Heatmap
- ggplot2
- Statistics
- Cluster
- File formats
- Misc
update all R packages
install.packages("rvcheck")
update_all()
- R for data science
- Cheatsheets by rstudio
- Hands-On Data Science with R
- DataPyR
- http://www.sthda.com/english/
- http://www.r-bloggers.com/search/ggplot2
- 10 R packages I wish I knew about earlier
- Great R packages for data import, wrangling & visualization
- R package development - the Leek group way!
- stringr - A fresh approach to string manipulation in R http://stringr.tidyverse.org
- Text Processing in R
- pystr - Python String Methods in R. http://cran.r-project.org/web/packages/pystr
- R语言基础知识-字符串的处理
docs
packages
data structure
- tibble - A tibble, or tbl_df, is a modern reimagining of the data.frame, keeping what time has proven to be effective, and throwing out what is not.
tools
- faster-data-manipulation-7-packages
- data-wrangling-cheatsheet.pdf
- tidyr tidyr is a reframing of reshape2 designed to accompany the tidy data framework, and to work hand-in-hand with magrittr and dplyr to build a solid pipeline for data analysis.
- dplyr-and-plyr, When I use plyr/dplyr，[Using dplyr, and a comparison with plyr.]http://scicomp2014.edc.uri.edu/posts/2014-04-14-Smith.html
- dplyr: How to do data manipulation with R
- Programming with dplyr
- normalising-data-within-groups, script
- broom - Convert Statistical Analysis Objects into Tidy Data Frames
docs
packages
- caret - (Classification And Regression Training) R package that contains misc functions for training and plotting classification and regression models
- ROCR - visualizing classifier performance in R, with only 3 commands
- xgboost - Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Flink and DataFlow
- Large number of images: http://rgm3.lab.nig.ac.jp/RGM/R_image_list
- Static and dynamic network visualization with R
- http://rcharts.io/gallery/
- corrplot
- ordination plots
- igraph, Network Analysis and Visualization with R and igraph
- Dendrogram: hclust
- factoextra - Visualization of the outputs of a multivariate analysis http://www.sthda.com
- Sankey from Scratch using rCharts, d3.js, and igraph
- largevis - This is an implementation of the largeVis algorithm described in (https://arxiv.org/abs/1602.00370). It also incorporates code for a very fast algorithm for estimating k-nearest neighbors.
- Vennerable - Vennerable provides Venn diagrams in R. It displays Venn and Euler diagrams for up to 9 different sets and using a variety of geometries. It allows the display of area-weighted Venn diagrams and allows fine graphical control over the result.
- alluvial - Alluvial diagrams (you can also use ggalluvial
misc
circos like
- rCircos: R package for circular plots. [last update: 2013]
- OmicCircos: R package for circular plots for omics data. vignette [last update: 2016-05]
- circlize - circular layout in R http://jokergoo.github.io/circlize
Shiny
- ComplexHeatmap
- pheatmap
Extended packages. More: RStartHere, ggally
- ggthemes - Some extra themes, geoms, and scales for ggplot2.
- hrbrthemes - Opinionated, typographic-centric ggplot2 themes and theme components
- ggsci - Scientific Journal and Sci-Fi Themed Color Palettes for ggplot2
- cowplot - provide a publication-ready theme for ggplot2. similar package: ggmatrix, ggpairs, ggscatmat
- ggfortify - Define fortify and autoplot functions to allow ggplot2 to handle some popular R packages. http://cos.name/2015/11/ggfortify-visualization-in-one-line-of-code/
- ggrepel - Repel overlapping text labels away from each other.
- ggalt - Extra Coordinate Systems, Geoms and Statistical Transformations for 'ggplot2' https://cran.rstudio.com/web/packages/ggalt/ggalt.pdf
- ggforce - aime primarily at ad hoc data visualization in order to investigate the data at hand, and less at utilities for composing custom plots a la D3.js.
- gganimate - Create easy animations with ggplot2
- ggord - a take on ordination plots using ggplot2
- gbiplot - A biplot based on ggplot2
- ggnet - Simple network plots with ggplot2 in R. Similar packages: ggnetworkmap, ggraph - Grammar of Graph Graphics
- ggvis- Interactive grammar of graphics for R
- ggcorr: correlation matrixes with ggplot2
- ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.
- ggsurv - survival curves with ggplot2
- ggExtra Add marginal histograms to ggplot2, and more ggplot2 enhancements http://daattali.com/shiny/ggExtra-ggMarginal-demo/
- ggradar - radar charts with ggplot2
- ggRandomForests : Visually Exploring Random Forests
- ggmcmc: Tools for Analyzing MCMC Simulations from Bayesian Inference
- ggalluvial - alluvial diagrams in ggplot2
Tutorial
- 使用ggplot2画图 - YGC
- ggplot2-cheatsheet
- Getting started with ggplot2
- Beautiful plotting in R: A ggplot2 cheatsheet
- Recreating a famous visualisation
- http://stackoverflow.com/questions/14379737/how-can-i-make-xlab-and-ylab-visible-when-using-theme-wsj-ggthemes
- How to format plots for publication using ggplot2 (with some help from Inkscape)
- Remove grid and background from plot (ggplot2)
- Colors
- ggplot2 - Easy way to mix multiple graphs on the same page
- 2D plot with histograms for each dimension
- R Recipe: Aligning Axes in ggplot2
- making-faceted-heatmaps-with-ggplot2/
- R语言：ggplot2精细化绘图——以实用商业化图表绘图为例
- Quick Multivariate data analysis (PCA, CA, MCA) and visualization
- The R Stats Package (Adjust P-values for Multiple Comparisons, 多重检验中的FDR错误控制方法与p-value的校正及Bonferroni校正)
- How can I do post-hoc pairwise comparisons in R?
- rio - A Swiss-army knife for data I/O
reads xlsx/xls library(xslx)
data <- read.xlsx("datafile.xlsx", 1)
library(gdata)
# Read first sheet
data <- read.xls("datafile.xls")
- How to summarize data by group in R?
- Error in eval(expr, envir, enclos) : object ‘X' not found solution:
ggplot(..., **environment = environment()**) - how to apply a function to every row of a matrix (or a data frame) in R
- How to apply function over each matrix element
- How do I pass variables to a custom function in ddply?
- R-Transposing a data frame