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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 ...
A violin plot (on the left) and a sina plot (on the right) for the same sample. A sina plot is a type of diagram in which numerical data are depicted by points distributed in such a way that the width of the point distribution is proportional to the kernel density.
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.
[1] [2] [3] Assuming a variable is homoscedastic when in reality it is heteroscedastic (/ ˌ h ɛ t ər oʊ s k ə ˈ d æ s t ɪ k /) results in unbiased but inefficient point estimates and in biased estimates of standard errors, and may result in overestimating the goodness of fit as measured by the Pearson coefficient.
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]
dplyr is an R package whose set of functions are designed to enable dataframe (a spreadsheet-like data structure) manipulation in an intuitive, user-friendly way. It is one of the core packages of the popular tidyverse set of packages in the R programming language. [1]
Galbraith plots are available within the metafor package in R, along with various other diagnostic and summary plots. MIX 2.0 Software to perform meta-analysis and create Galbraith plots in Excel. RadialPlotter Java application for fission track, luminescence and other radial plots from P. Vermeesch.
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.