Zuguang Gu

Zuguang Gu

6 packages on CRAN

5 packages on Bioconductor

CePa

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Use pathway topology information to assign weight to pathway nodes.

circlize

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Circular layout is an efficient way for the visualization of huge amounts of information. Here this package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data. The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.

GetoptLong

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This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.

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It provides more configurations on the option values such as validation and filtering on the values, making options invisible or private.

ComplexHeatmap

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Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.

EnrichedHeatmap

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Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.

gtrellis

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Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

HilbertCurve

bioconductor
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Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve.

pkgndep

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It checks the heaviness of the packages that user's package depends on. For each package listed in the "Depends", "Imports" and "Suggests" fields in the DESCRIPTION file, it opens a new R session, loads the package and counts the number of namespaces that are loaded. The summary of the dependencies is visualized by a customized heatmap. Examples of dependency analysis can be found at <https://jokergoo.github.io/pkgndep/stat/>.

rGREAT

bioconductor
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This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user's input and automatically retrieving results from GREAT web server.

dendextend

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Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.