Function

CircosArc()

CircosArc() can display the CNV without value, Gene domain, Chromosome band, etc.

Example of CircosArc()

library(interacCircos)
arcData=arcExample
Circos(moduleList=CircosArc('Arc01', outerRadius = 212, 
innerRadius = 224, data=arcData,animationDisplay = TRUE),
genome=list("EGFR"=1211),
outerRadius = 220,genomeFillColor = c("grey"),
ARCMouseOverDisplay = TRUE,ARCMouseOverTooltipsSetting = "style1",
ARCMouseOutDisplay = TRUE,ARCMouseOutColor = NULL)

Note : No data input for CircosArc(). The details for parameters are available by ?CircosArc().

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CircosAuxLine()

CircosAuxLine() can display Auxiliary line for better explain the relationship between modules.

Example of CircosAuxLine()

library(interacCircos)

Circos(moduleList=CircosAuxLine('AuxLine01',
animationDisplay = TRUE,animationType = "linear",
animationDelay =0,animationTime = 1000))

Note : No data input for CircosAuxLine(). The details for parameters are available by ?CircosAuxLine().

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CircosBackground()

CircosBackground() can display background and axis circles for other functions.

Example of CircosBackground()

library(interacCircos)

Circos(moduleList=CircosBackground('bg01', fillColors="#FFEEEE", 
borderSize = 1,animationDisplay = TRUE))

Note : No data input for CircosBackground(). The details for parameters are available by ?CircosBackground().

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CircosBubble()

CircosBubble() can display the gene expression data as well as its classification, etc.

Example of CircosBubble()

library(interacCircos)

bubbleData=bubbleExample
Circos(moduleList=CircosBubble('Bubble01', maxRadius = 230, 
minRadius = 170, data=bubbleData, blockStroke = TRUE, bubbleMaxSize =10, 
bubbleMinSize = 2, maxColor = "red", minColor = "yellow", totalLayer =3, 
animationDisplay = TRUE, animationType="linear"),
genome = list("2L"=23011544,"2R"=21146708,
"3L"=24543557,"3R"= 27905053,"X"=22422827,"4"=1351857), 
BUBBLEMouseOverDisplay =TRUE,BUBBLEMouseOverTooltipsSetting = "style1",
innerRadius = 236,BUBBLEMouseOutDisplay = TRUE,BUBBLEMouseOutColor = NULL)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosBubble().

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CircosChord()

CircosChord() can display the relationship between gene, exon, protein, etc. (Using matrix as chord path)

Example of CircosChord()

library(interacCircos)

chordData=chordExample
Circos(moduleList=CircosChord('CHORD01', data = chordData,innerRadius= 210,outerRadius= 211,fillOpacity=0.67,
strokeColor="black",strokeWidth= "1px",outerARCText=FALSE,autoFillColor = FALSE,
fillColor = c("blue","green","yellow","red","purple","grey","orange")),
genome=list("C.CK" = 189.51,"C.NPK"=188,"GC.CK"=186.11,
"GC.NPK"=191.51,"Alphaproteobacteria"=70.16,"Betaproteobacteria"=23.51,"Gammaproteobacteria"=25.51,
"Deltaproteobacteria"=23.28,"Acidobacteria"=53.62,"Actinobacteria"=72.33,"Bacteroidetes"=22.41,
"Chloroflexi"=15.08,"Firmicutes"=10.72,"Gemmatimonadetes"=26.37,"Planctomycetes"=19.26,"Thaumarchaeota"=6.15,
"Verrucomicrobia"=8.3,"Ascomycota"=159.41,"Basidiomycota"=79.73,"Zygomycota"=139.29 ),outerRadius = 217,
genomeLabelDisplay = FALSE,CHORDMouseEvent =TRUE,CHORDMouseOverDisplay = TRUE)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosChord().

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CircosChord.p()

CircosChord.p() can display the relationship between gene, exon, protein, etc. (Using start/end position as chord path)

Example of CircosChord.p()

library(interacCircos)

chordData=chord.pExample

Circos(moduleList=CircosChord.p('CHORD01', data = chordData,radius= 216,opacity=0.67, 
color="black"), innerRadius = 217, outerRadius = 237,genomeLabelDisplay = TRUE,zoom=FALSE)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosChord.p().
CircosChord.p() now is not compatible with zoom and compare function of BioCircos.js/NG-Circos

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CircosCnv()

CircosCnv() can display the CNV data, etc.

Example of CircosCnv()

library(interacCircos)

cnvData=cnvExample
Circos(moduleList=CircosCnv('Cnv01',maxRadius =175, minRadius =116, 
data =cnvData,width=2,color = "#4876FF",animationDisplay = TRUE,
animationType = "linear",animationTime = 500)+
CircosBackground("bg01",minRadius = 116,maxRadius = 175,
fillColors = "#F2F2F2",axisShow = TRUE),CNVMouseOverDisplay = TRUE,
CNVMouseOverTooltipsSetting = "style1",CNVMouseOutDisplay = TRUE,
CNVMouseOutColor = NULL)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosCnv().

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CircosGene()

CircosGene() can display the gene profile, transcript profile, RNA profile, etc.

Example of CircosGene()

library(interacCircos)

geneData=geneExample
Circos(moduleList=CircosGene('Gene01', outerRadius = 195, innerRadius = 180, 
data=geneData,arrowGap = 10, arrowColor = "black",arrowSize = "12px",
cdsColor = "#1e77b3",cdsStrokeColor = "#1e77b3",cdsStrokeWidth= 0,
utrWidth= 0,utrColor= "#fe7f0e",utrStrokeColor= "#fe7f0e",
animationDisplay = TRUE),genome =list("EGFR"=1000),outerRadius = 220,
GENEMouseOverDisplay = TRUE,GENEMouseOverTooltipsSetting = "style1",
GENEMouseOutDisplay = TRUE,GENEMouseOutColor = NULL)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosGene().

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CircosHeatmap()

CircosHeatmap() can display the gene expression, probe signal, etc.

Example of CircosHeatmap()

library(interacCircos)

heatmapData=heatmapExample
Circos(moduleList=CircosHeatmap('Heatmap01', maxRadius= 180, minRadius = 100, 
data=heatmapData,totalLayer = 3,animationDisplay = TRUE),
genome = list("2L"=23011544,"2R"=21146708,"3L"=24543557,"3R"=27905053,
"4"=1351857,"X"=22422827),HEATMAPMouseEvent = TRUE,HEATMAPMouseOverDisplay = TRUE,
HEATMAPMouseOverTooltipsSetting = "style1",HEATMAPMouseOutDisplay = TRUE,
HEATMAPMouseOutColor = NULL)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosHeatmap().

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CircosHistogram()

CircosHistogram() can display the gene expression, probe signal, etc.

Example of CircosHistogram()

library(interacCircos)

histogramData=histogramExample
Circos(moduleList=CircosHistogram('HISTOGRAM01', data = histogramData,
fillColor= "#ff7f0e",maxRadius = 210,minRadius = 175,
animationDisplay = TRUE),genome=list("2L"=23011544,"2R"=21146708,"3L"=24543557,
"3R"= 27905053,"X"=22422827,"4"=1351857),outerRadius = 220,
HISTOGRAMMouseOverDisplay = TRUE,HISTOGRAMMouseOverTooltipsSetting = "style1",
HISTOGRAMMouseOutDisplay = TRUE,HISTOGRAMMouseOutColor = NULL)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosHistogram().

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CircosLegend()

CircosLegend() can display legend easily for better explain each element.

Example of CircosLegend()

library(interacCircos)

legend1 = list(type= "circle", color="#1E77B4",opacity="1.0",
circleSize="8",text= "C.CK", textSize= "14",textWeight="normal")
legend2 = list(type= "circle", color="#AEC7E8",opacity="1.0",
circleSize="8",text= "C.NPK", textSize= "14",textWeight="normal")
Circos(moduleList=CircosLegend('legend01', title = "legend",
data=list(legend1,legend2),size = 20))

Note : No data should be input. The details for parameters are available by ?CircosLegend().

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CircosLine()

CircosLine() can display the gene expression, r2 value, etc.

Example of CircosLine()

library(interacCircos)

lineData=lineExample
Circos(moduleList=CircosLine('LINE01', data = lineData,
maxRadius=200,minRadius=150,color= "#ff0031",
animationDisplay = TRUE,animationTime = 4000,animationDelay = 100)+
CircosBackground('BG01',minRadius = 205,maxRadius = 150),
LINEMouseOverDisplay = TRUE,LINEMouseOverTooltipsSetting = "style1",
LINEMouseOutDisplay = TRUE,LINEMouseOutLineStrokeColor = NULL)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosLine().

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CircosLink() can display the gene fusions, interaction, SV data, etc.

Example of CircosLink()

library(interacCircos)

linkData=linkExample
Circos(moduleList=CircosLink('LINK01', data = linkData,
LinkRadius= 140,fillColor= "#9e9ac6",width= 2,
axisPad= 3,labelPad=8,animationDisplay=TRUE,
animationDirection="1to2",animationType= "linear" ),
LINKMouseOverTooltipsSetting = "style1",LINKMouseOverDisplay=TRUE,
LINKMouseOutDisplay = TRUE)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosLink().

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CircosLollipop()

CircosLollipop() can display the somatic mutation, germline variantion, etc.

Example of CircosLollipop()

library(interacCircos)

lollipopData=lollipopExample
arcData=arcExample
Circos(moduleList=CircosLollipop('Lollipop01', 
data=lollipopData, fillColor="#9400D3",circleSize= 6, 
strokeColor= "#999999", strokeWidth= "1px", 
animationDisplay=TRUE, lineWidth= 2,realStart= 101219350)+
CircosArc('Arc01', outerRadius = 212, innerRadius = 224, data=arcData),
genome=list("EGFR"=1211),outerRadius = 220,genomeFillColor = c("grey"),
LOLLIPOPMouseOverDisplay = TRUE,LOLLIPOPMouseOverTooltipsSetting = "style1",
LOLLIPOPMouseOutDisplay = TRUE,LOLLIPOPMouseOutColor = NULL,
LOLLIPOPMouseOutCircleSize = 6,LOLLIPOPMouseOutCircleStrokeWidth = "1px",
LOLLIPOPMouseOutCircleStrokeColor = "#999999")

Note : The data is input through the data parameter. The details for parameters are available by ?CircosLollipop().

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CircosScatter()

CircosScatter() can display the SNP without value, Genes data, etc.

Example of CircosScatter()

library(interacCircos)

scatterData=scatterExample
Circos(moduleList=CircosScatter('SCATTER01', data = scatterData,
radius=180,innerCircleColor= "#3d6390",outerCircleColor= "#99cafe",
random_data= 40,animationDisplay = TRUE,animationDelay = 10,
animationTime = 1000,animationType = "linear"),SCATTERMouseOverDisplay = TRUE,
SCATTERMouseOverTooltipsSetting = "style1",SCATTERMouseOutDisplay = TRUE,
SCATTERMouseOutColor = NULL,SCATTERMouseOutCircleStrokeColor ="#99cafe",
SCATTERMouseOutCircleStrokeWidth = 6)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosScatter().

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CircosSnp()

CircosSnp() can display the SNP density data, GWAS data, etc.

Example of CircosSnp()

library(interacCircos)

snpData=snpExample
Circos(moduleList=CircosSnp('SNP01', minRadius =150, 
maxRadius = 190, data = snpExample,SNPFillColor= "#9ACD32", 
circleSize= 2, SNPAxisColor= "#B8B8B8", SNPAxisWidth= 0.5, 
animationDisplay=TRUE,animationTime= 2000, animationDelay= 0, 
animationType= "linear") + 
CircosBackground('BG01',minRadius = 145,maxRadius = 200),
SNPMouseOverDisplay = TRUE,SNPMouseOverTooltipsSetting = "style1",
SNPMouseOutDisplay = TRUE,SNPMouseOutColor = NULL)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosSnp().

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CircosText()

CircosText() can display annotation text at specific elements.

Example of CircosText()

library(interacCircos)

Circos(moduleList=CircosText('text01', 'Annotation',
 color = '#DD2222', x = -40,animationDisplay = TRUE,
 animationInitialPositionX = 200))

Note : No data should be input. The details for parameters are available by ?CircosText().

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CircosWig()

CircosWig() can display the gene expression data, read depth etc.

Example of CircosWig()

library(interacCircos)

wigData=wigExample
Circos(moduleList=CircosWig('WIG01', data = wigData, 
maxRadius= 200,minRadius= 150,strokeColor= "darkblue",
color= "lightblue",strokeType= "cardinal",
animationDisplay = TRUE,animationTime = 3000,animationType="linear")+
CircosBackground('BG01',minRadius = 205,maxRadius = 150),
genome=list("chr8"=1000),outerRadius = 220,WIGMouseOverDisplay = TRUE,
WIGMouseOverTooltipsSetting = "style1",WIGMouseOutDisplay = TRUE,
WIGMouseOutFillColor = NULL)

Note : The data is input through the data parameter. The details for parameters are available by ?CircosWig().

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