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ggplot2 is an open-source data visualization package for the statistical programming language R.Created by Hadley Wickham in 2005, ggplot2 is an implementation of Leland Wilkinson's Grammar of Graphics—a general scheme for data visualization which breaks up graphs into semantic components such as scales and layers. ggplot2 can serve as a replacement for the base graphics in R and contains a ...
UpSet plots became popular as they became available as an R-library based on ggplot2, [3] and were subsequently re-implemented in various programming languages, such as Python, and others. [4] As of January 2024, UpSetR has been downloaded from CRAN more than 1.5 million times, although it was last updated 5 years ago. [5]
This book also served as the foundation for the R package ggplot2, [8] the Python Bokeh package, [9] the R package ggbio, [10] the Vega declarative language, and helped shape the Polaris project at Stanford University. [11]
R is a programming language for statistical computing and data visualization. It has been adopted in the fields of data mining, bioinformatics and data analysis. [9] The core R language is augmented by a large number of extension packages, containing reusable code, documentation, and sample data. R software is open-source and free software.
There is also an active R community around the tidyverse. For example, there is the TidyTuesday social data project organised by the Data Science Learning Community (DSLC), [16] where varied real-world datasets are released each week for the community to participate, share, practice, and make learning to work with data easier. [17]
Violin plots are similar to box plots, except that they also show the probability density of the data at different values, usually smoothed by a kernel density estimator.A violin plot will include all the data that is in a box plot: a marker for the median of the data; a box or marker indicating the interquartile range; and possibly all sample points, if the number of samples is not too high.
By minimizing these systematic variations, true biological differences can be found. To determine whether normalization is needed, one can plot Cy5 (R) intensities against Cy3 (G) intensities and see whether the slope of the line is around 1. An improved method, which is basically a scaled, 45 degree rotation of the R vs. G plot is an MA-plot. [4]
The following example illustrates this by applying the second SMAPE formula: Over-forecasting: A t = 100 and F t = 110 give SMAPE = 4.76% Under-forecasting: A t = 100 and F t = 90 give SMAPE = 5.26%.