CircosAPI

namespace: SMRUCC.genomics.Visualize.Circos

Shoal shell interaction with circos perl program to draw a circle diagram of a bacteria genome.

Methods

__geneHighlights

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.__geneHighlights(System.Collections.Generic.IEnumerable{SMRUCC.genomics.Assembly.NCBI.GenBank.CsvExports.GeneDumpInfo},System.Collections.Generic.Dictionary{System.String,System.String},SMRUCC.genomics.ComponentModel.Loci.Strands)

生成基因组的基因片段

Parameter Name Remarks
anno -
Colors -
Strands -

CreateDoc

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.CreateDoc

Creats a new @”T:SMRUCC.genomics.Visualize.Circos.Configurations.Circos” plots configuration document.
returns: @”M:SMRUCC.genomics.Visualize.Circos.Configurations.Circos.CreateObject”

GenerateBlastnAlignment

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.GenerateBlastnAlignment(SMRUCC.genomics.Visualize.Circos.Configurations.Circos,SMRUCC.genomics.Interops.NCBI.Extensions.NCBIBlastResult.AlignmentTable,System.Double,System.Double,SMRUCC.genomics.Visualize.Circos.TrackDatas.Highlights.IdentityColors)

The blast result alignment will be mapping on the circos plot circle individual as the highlights element in the circos plot.

Parameter Name Remarks
doc -
table -
r1 -
rInner -

GenerateGeneCircle

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.GenerateGeneCircle(SMRUCC.genomics.Visualize.Circos.Configurations.Circos,System.Collections.Generic.IEnumerable{SMRUCC.genomics.Assembly.NCBI.GenBank.CsvExports.GeneDumpInfo},System.Boolean,System.String,System.Boolean,System.Boolean,System.Boolean)
Parameter Name Remarks
doc -
anno -
IDRegex 基因的名称的正则表达式解析字符串。如果为空字符串,则默认输出全部的名称
onlyGeneName 当本参数为真的时候, IDRegex 参数失效

GetIdeogram

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.GetIdeogram(SMRUCC.genomics.Visualize.Circos.Configurations.Circos)

还没有ideogram文档的时候,则会返回一个新的文档

Parameter Name Remarks
doc -

RNAVisualize

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.RNAVisualize(SMRUCC.genomics.Visualize.Circos.Configurations.Circos,SMRUCC.genomics.Assembly.NCBI.GenBank.TabularFormat.PTT)

使用Highlighs来显示RNA分子在基因组之上的位置

SetBasicProperty

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.SetBasicProperty(SMRUCC.genomics.Visualize.Circos.Configurations.Circos,SMRUCC.genomics.SequenceModel.FASTA.FastaToken,System.Collections.Generic.IEnumerable{Microsoft.VisualBasic.ComponentModel.TripleKeyValuesPair},System.Int32)
Parameter Name Remarks
doc -
NT -
Bands -
loophole 默认为0,没有缺口

SetIdeogramRadius

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.SetIdeogramRadius(SMRUCC.genomics.Visualize.Circos.Configurations.Ideogram,System.Double)

其他的圆圈都会发生变化,则每一次修改之后都需要重新计算圆圈的位置

Parameter Name Remarks
doc -
r -

圆圈的最大值只能够到达1.2了???
相对的大小是和ideogram有关的
1/ideogram.radius

SetIdeogramWidth

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.SetIdeogramWidth(SMRUCC.genomics.Visualize.Circos.Configurations.Ideogram,System.Int32)

Invoke set the ideogram width in the circos plot drawing, if the width value is set to ZERO,
then the ideogram circle will be empty on the drawing but this is different with the ideogram
configuration document was not included in the circos main configuration.

Parameter Name Remarks
doc -
width -

SetPlotElementOrientation

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.SetPlotElementOrientation(SMRUCC.genomics.Visualize.Circos.Configurations.Nodes.Plots.ITrackPlot,System.String)
Parameter Name Remarks
Element -
Orientation -

setProperty

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.setProperty(SMRUCC.genomics.Visualize.Circos.Configurations.Circos,System.String,System.String)

Invoke set of the property value in the circos document object.

Parameter Name Remarks
doc -
name -
value -

SetRadius

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.SetRadius(SMRUCC.genomics.Visualize.Circos.Configurations.Circos,System.Collections.Generic.IEnumerable{System.Double[]})
Parameter Name Remarks
doc -
r 从外圈到内圈的

WriteData

1
SMRUCC.genomics.Visualize.Circos.CircosAPI.WriteData(SMRUCC.genomics.Visualize.Circos.Configurations.Circos,System.String,System.Boolean)

Save the circos plots configuration object as the default configuration file: circos.conf

Parameter Name Remarks
doc -
outDIR -
Debug -

Properties

null

This property have no data value