• Stars
    star
    135
  • Rank 259,688 (Top 6 %)
  • Language
    R
  • License
    Other
  • Created almost 3 years ago
  • Updated 2 months ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Visualize data on spirals

Visualize Data on Spirals

R-CMD-check CRAN CRAN

Features

The package spiralize visualizes data along an Archimedean spiral. It has two major advantages for visualization:

  1. It is able to visualize data with very long axis with high resolution.
  2. It is efficient for time series data to reveal periodic patterns.

Citation

Zuguang Gu, et al., spiralize: an R package for Visualizing Data on Spirals, Bioinformatics, 2021. https://doi.org/10.1093/bioinformatics/btab778

Install

The package is available on CRAN and can be installed by:

install.packages("spiralize")

If you want the latest version, install it directly from GitHub:

library(devtools)
install_github("jokergoo/spiralize")

Usage

It includes three steps:

  1. initialize the spiral,
  2. add a track,
  3. add graphics in the track.

Step 2 and 3 can be applied multiple times to allow multiple-track visualization along the spiral.

The code for making spiral plot looks like follows:

library(spiralize)
spiral_initialize(...)
spiral_track(...)
spiral_points(...)
...

Graphics

Complex plots are baiscally constructed from simple graphics. Here there are following low-level graphics functions:

  • spiral_points()
  • spiral_lines()
  • spiral_rect()
  • spiral_segments()
  • spiral_polygon()
  • spiral_bars()
  • spiral_text()
  • spiral_axis()
  • spiral_yaxis()
  • spiral_raster()

Particularlly, horizon chart is very suitable to put on the spiral, thus there is one function for this:

  • spiral_horizon()

Spiral plot can also visualize dendrograms with large number of leaves, thus there are following two functions:

  • spiral_dendrogram()
  • spiral_phylo()

Vignettes

There are the following vignettes:

Examples

  1. Difference of ggplot2 daily downloads to the mean of the current year (2015-2021). Each loop contains 52 weeks so that same weeks in different years locate at the same angle in the polar coordinates.

image

  1. The same data as the first one, but horizon chart is used. Also title and legends are added.

image

  1. A phylogenetic life tree with 50645 species.

download

  1. The spiral COVID-19 Shiny app

https://jokergoooo.shinyapps.io/covid19/

covid19_spiral

License

MIT @ Zuguang Gu

More Repositories

1

ComplexHeatmap

Make Complex Heatmaps
R
1,204
star
2

circlize

Circular visualization in R
R
928
star
3

EnrichedHeatmap

make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.
R
180
star
4

InteractiveComplexHeatmap

Make Interactive Complex Heatmaps
R
116
star
5

simplifyEnrichment

Simplify functional enrichment results
R
94
star
6

rGREAT

GREAT Analysis - Functional Enrichment on Genomic Regions
R
74
star
7

cola

A General Framework for Consensus Partitioning
HTML
57
star
8

pkgndep

Analyzing Dependency Heaviness of R Packages
R
44
star
9

HilbertCurve

Visualize genomic data by Hilbert curve
R
40
star
10

gtrellis

Genomic plot in trellis layout
R
39
star
11

circlize_book

Documentation for circlize package
HTML
36
star
12

KeywordsEnrichment

R
30
star
13

bsub

Send R code/R scripts/shell commands to LSF cluster without leaving R
R
22
star
14

ComplexHeatmap-reference

Documentation of ComplexHeatmap package
HTML
21
star
15

GetoptLong

Parse command-line arguments and simple variable interpolation
R
16
star
16

ComplexHeatmap_v2_paper_code

R
15
star
17

GSEAtraining

HTML
14
star
18

circlize_examples

circlize examples
HTML
12
star
19

BioMartGOGeneSets

Gene Ontology Gene Sets from BioMart
R
10
star
20

ComplexHeatmap-examples

R
10
star
21

BioCartaImage

BioCarta pathway images
R
9
star
22

jokergoo

9
star
23

ngspipeline

NGS pipeline
Perl
9
star
24

IlluminaHumanMethylationEPICv2anno.20a1.hg38

R
8
star
25

Crypt-DNASequence

Encrypt and decrypt strings to DNA Sequences
Perl
8
star
26

Useful_R_packages

8
star
27

GlobalOptions

Generate function to get or set global options
R
8
star
28

simona

Semantic Similarity in Bio-Ontologies
R
7
star
29

IlluminaHumanMethylationEPICv2manifest

R
6
star
30

cola_hcp

Hierarchical Consensus Partitioning
5
star
31

jokergoo.github.io

Personal website
HTML
4
star
32

spiralize_vignettes

Vignettes of the spiralize package
HTML
4
star
33

pheatmap2

pretty and parallel heatmap
R
4
star
34

GeneSummary

RefSeq gene summary
R
2
star
35

BioMartGOGeneSets_data

2
star
36

cotools

NGS tools for Conputational Oncology group in DKFZ
R
2
star
37

cola_manuscript

Scripts for the cola manuscript
R
2
star
38

UniProtKeywords

Keywords from the UniProt database
R
2
star
39

supplementary

HTML
2
star
40

simplifyEnrichment_supplementary

Supplementary for simplifyEnrichment manuscript
HTML
2
star
41

cola_examples

Examples of cola analysis
HTML
2
star
42

CePa

Centrality-based pathway enrichment
R
2
star
43

colorRamp2

Generate Color Mapping Functions
R
1
star
44

cola_vignettes

Vignettes of the cola package
HTML
1
star
45

gsubeval

Substitute with an Evaluated Expression
R
1
star
46

GTF

Simple class to process GTF data
R
1
star
47

top2pct_scientists

top2pct_scientists
R
1
star
48

epik

Integrative analysis for epigenomic sequencing data
HTML
1
star
49

simona_supplementary

HTML
1
star
50

List-Vectorize

vectorized functions in perl
Perl
1
star
51

Statistics-Multtest

Control false discovery rate in multiple test
Perl
1
star
52

Microarray-GEO-SOFT

Reading microarray data in SOFT format from GEO database
Perl
1
star