Quick Start

I. Installation

interacCircos is available at Github /Bioconductor or you can download here

Install from Github

# Install devtools first!
if (!require('devtools')){install.packages('devtools')}

devtools::install_github('mrcuizhe/interacCircos')

# R package of htmlwidgets, RColorBrewer, plyr, jsonlite
# and grDevices are required !

Install from local package

#Download interacCircos package to local disk first!

install.packages("PATH/TO/PACKAGE/interacCircos_X.X.X.tar.gz", repos = NULL, 
type = "source")

# R package of htmlwidgets, RColorBrewer, plyr, jsonlite
# and grDevices are required !

Install from Bioconductor

#Install Bioconductor first!

if (!requireNamespace("BiocManager", quietly = TRUE))
    {install.packages("BiocManager")}

BiocManager::install("interacCircos")

# R package of htmlwidgets, RColorBrewer, plyr, jsonlite
# and grDevices are required !  
# Bioconductor version: ≥ Release (3.13)
# R version ≥ 4.1

II. Overview

If you are a NG-Circos/BioCircos.js/circosJS user and familiar with the modules and their data structure, it will only take you a few moment for getting used to interacCircos.

a main function called Circos() is necessary to display the genome for Circos plot, which is the coordinates basis for all modules.

Up to 21 types of modules can be added to genome track through a parameter in Circos() called moduleList. Modules can be added by simply using "+" in moduleList. For example, moduleList=CircosText()+CircosBackground() means apply one TEXT module and one BACKGROUND module together to genome track. The other parameters in Circos() are all correspond to that in NG-Circos/BioCircos.js/circosJS one to one.

Note that for 3 of all modules(COMBINATION, COMPARE, REDIRECT from NG-Circos) , their parameters are included in Circos()

For the other 18 of 21 modules, which has an independent function(CircosArc(), CircosAuxLine(), CircosBackground(), CircosBubble(), CircosChord(), CircosChord.p(), CircosCnv(), CircosGene(), CircosHeatmap(), CircosHistogram(), CircosLegend(), CircosLine(), CircosLink(), CircosLollipop(), CircosScatter(), CircosSnp(), CircosText(), CircosWig() from NG-Circos/BioCircos.js/circosJS), all data(if needed) are input through a parameter called data in a data.frame structure and all parameters are correspond to that in JacaScript version.

III. 2 steps of drawing interactive plot

Step 1. Genome configuration

Default genome track

library(interacCircos)

Circos(zoom=FALSE)

Plot viewer

Try changing genome list and its color

The genome is set by default as hg19, the genome can be changed by setting genome=list("Example1"=100,"Example2"=200,"Example3"=300). Meanwhile, the color of each chromosome can be changed by setting genomeFillColor = c("red","blue","green")

library(interacCircos)

Circos(zoom = FALSE,genome=list("Example1"=100,"Example2"=200,
"Example3"=300),genomeFillColor = c("red","blue","green"))

Plot viewer

Try automatically filling genome color

The filling color for chromosome can also be set automatically by choosing a RColorBrewer palette, such as Blues

library(interacCircos)

Circos(zoom = FALSE,genome=list("Example1"=100,"Example2"=200,
"Example3"=300),genomeFillColor = "Blues")

Plot viewer

Find more parameters

Other parameters are all documented and try ?Circos() for details

library(interacCircos)

Circos(zoom=FALSE,genome=list("Example1"=100,"Example2"=200,
"Example3"=300),genomeFillColor = "Blues",chrPad = 0,genomeTicksDisplay = TRUE,
genomeTicksScale = 10,genomeLabelDisplay = FALSE)

Plot viewer

Step 2. Add function for more plot tracks

Each plot function (e.g. Module of NG-Circos) is added through moduleList, a parameter of Circos()

Totally 18 modules:
    CircosArc()
    CircosAuxLine()
    CircosBackground()
    CircosBubble()
    CircosChord()
    CircosChord.p()
    CircosCnv()
    CircosGene()
    CircosHeatmap()
    CircosHistogram()
    CircosLegend()
    CircosLine()
    CircosLink()
    CircosLollipop()
    CircosScatter()
    CircosSnp()
    CircosText()
    CircosWig()
can be added by using "+" in moduleList

IV. Plot saving

If you are using RStudio, the plot can be saved as an image or a html page directly from viewer panel.

If you are using R in command, the plot can be saved as a html page, thanks to the htmlwidgets library

library(interacCircos)
library(htmlwidgets)

plot <- Circos(zoom=FALSE,genome=list("Example1"=100,"Example2"=200,
"Example3"=300),genomeFillColor = "Blues",chrPad = 0,genomeTicksDisplay = TRUE,
genomeTicksScale = 10,genomeLabelDisplay = FALSE)

saveWidget(plot, "plot.html")

The plot will be saved at your current directory