Create interactive Q-Q, manhattan and volcano plots that are usable from the R console, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a point to show details or drag a rectangle to zoom. A manhattan plot is a popular graphical method for visualizing results from high-dimensional data analysis such as a (epi)genome wide association study (GWAS or EWAS), in which p-values, Z-scores, test statistics are plotted on a scatter plot against their genomic position. Manhattan plots are used for visualizing potential regions of interest in the genome that are associated with a phenotype. Interactive manhattan plots allow the inspection of specific value (e.g. rs number or gene name) by hovering the mouse over a cell, as well as zooming into a region of the genome (e.g. a chromosome) by dragging a rectangle around the relevant area. This work is based on the 'qqman' package by Stephen Turner and the 'plotly.js' engine. It produces similar manhattan and Q-Q plots as the 'manhattan' and 'qq' functions in the 'qqman' package, with the advantage of including extra annotation information and interactive web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
|Author||Sahir Bhatnagar [aut, cre] (http://sahirbhatnagar.com/)|
|Date of publication||2016-11-16 01:56:53|
|Maintainer||Sahir Bhatnagar <email@example.com>|
|License||MIT + file LICENSE|
HapMap: Subset of HapMap data with simulated GWAS results
manhattanly: Creates a plotly manhattan plot
manhattanr: Creates a manhattanr object
qqly: Creates a plotly Q-Q plot
qqr: Creates a qq object
significantSNP: Character vector of SNPs to highlight
volcanoly: Creates a plotly volcano plot
volcanor: Creates a volcano object
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