CircosAPI

Full name SMRUCC.genomics.Visualize.Circos.CircosAPI Assembly SMRUCC.genomics.Visualize.Circos.Core Members 21

01 Syntax

SMRUCC.genomics.Visualize.Circos.CircosAPI

02 Methods

Name	Overloads	Summary
SetIdeogramWidth	1	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 i…
setProperty	1	Invoke set of the property value in the circos document object.
SetIdeogramRadius	1	Invoke set the radius value of the ideogram circle.
SetRadius	2
PlotsSeperatorLine	1	Creates a new seperator object in the circos plot with the specific width of the line, default is ZERO, not display.
AddMotifSites	1	Mapping details: IMotifSite.family -> Color IMotifSite.name -> display title label
RNAVisualize	1	使用Highlighs来显示RNA分子在基因组之上的位置
GenerateGeneCircle	1
CreateGenomeCircle	1	Creates the circos outside gene circle from the export csv data of the genbank database file.
AddPlotTrack	1	Adds a new circos plots element into the circos.conf object.
SetBasicProperty	1
SkeletonFromDoor	1	Creates the basic KaryotypeEntry document for the circos plot.
WriteData	1	Save the circos plots configuration object as the default configuration file: circos.conf
RemoveTicks	1	Removes the ticks label from the circos docuemnt node.
RemoveIdeogram	1	Removes the ideogram plots element from the circos document node.
Shell	1	Invoke the circos command line program for drawing the circos plots.

03 Fields

Name	Overloads	Summary
null	2	This property have no data value
yes	1
no	1

04 Members

method SetIdeogramWidth #

SetIdeogramWidth(IdeogramInclude, 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.

Parameters

Name	Type	Description
`idg`	IdeogramInclude	-
`width`	`Int32`	-

method setProperty #

setProperty(Circos, String, String)

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

Parameters

Name	Type	Description
`circos`	Circos	-
`name`	`String`	The property name in the circos document object, case insensitive.
`value`	`String`	String value of the circos document object property.

method SetIdeogramRadius #

SetIdeogramRadius(IdeogramInclude, Double)

Invoke set the radius value of the ideogram circle. (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)

Remarks

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

Parameters

Name	Type	Description
`ideogram`	IdeogramInclude	-
`r`	`Double`	-

method SetRadius #

SetRadius(Circos, IEnumerable(Of Double()))

Parameters

Name	Type	Description
`circos`	Circos	-
`r`	`IEnumerable(Of Double())`	从外圈到内圈的

method PlotsSeperatorLine #

PlotsSeperatorLine(Int32, Int32)

Creates a new seperator object in the circos plot with the specific width of the line, default is ZERO, not display.

Parameters

Name	Type	Description
`Length`	`Int32`	-
`width`	`Int32`	-

method AddMotifSites #

AddMotifSites(Circos, IEnumerable(Of IMotifSite), Boolean)

Mapping details:

 [IMotifSite.family](cref:P:SMRUCC.genomics.ComponentModel.Loci.IMotifSite.family) -> [Color](cref:T:System.Drawing.Color)
 [IMotifSite.name](cref:P:SMRUCC.genomics.ComponentModel.Loci.IMotifSite.name) -> display title label

Parameters

Name	Type	Description
`circos`	Circos	-
`motifs`	`IEnumerable(Of IMotifSite)`	-
`snuggle_refine`	`Boolean`	-

method RNAVisualize #

RNAVisualize(Circos, PTT)

使用Highlighs来显示RNA分子在基因组之上的位置

method GenerateGeneCircle #

GenerateGeneCircle(Circos, IEnumerable(Of GeneTable), Boolean, String, Boolean, Boolean, Boolean, Dictionary(Of String, String))

Parameters

Name	Type	Description
`doc`	Circos	-
`anno`	`IEnumerable(Of GeneTable)`	-
`IDRegex`	`Boolean`	Regular expression for parsing the number value in the gene's locus_tag. (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`	`String`	当本参数为真的时候， IDRegex 参数失效

method CreateGenomeCircle #

CreateGenomeCircle(IEnumerable(Of GeneTable), FastaSeq, String)

Creates the circos outside gene circle from the export csv data of the genbank database file.

Parameters

Name	Type	Description
`anno`	`IEnumerable(Of GeneTable)`	-
`genome`	`FastaSeq`	-
`defaultColor`	`String`	-

method AddPlotTrack #

AddPlotTrack(Circos, ITrackPlot)

Adds a new circos plots element into the circos.conf object.

Parameters

Name	Type	Description
`circos`	Circos	-
`track`	ITrackPlot	-

method SetBasicProperty #

SetBasicProperty(Circos, FastaSeq, IEnumerable(Of NamedTuple(Of String)), Int32)

Parameters

Name	Type	Description
`circos`	Circos	-
`NT`	`FastaSeq`	-
`bands`	`IEnumerable(Of NamedTuple(Of String))`	-
`loopHole`	`Int32`	默认为0，没有缺口

method SkeletonFromDoor #

SkeletonFromDoor(Circos, FastaSeq, String, Int32)

Creates the basic KaryotypeEntry document for the circos plot.

Parameters

Name	Type	Description
`doc`	Circos	-
`NT`	`FastaSeq`	-
`DOOR`	`String`	-
`loophole`	`Int32`	-

method WriteData #

WriteData(Circos, String, String, DebugGroups)

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

Parameters

Name	Type	Description
`circos`	Circos	-
`outDIR`	`String`	-
`debug`	`String`	-
`circosScriptPath`	DebugGroups	The file path of the circos executable program(`bin\circos.exe`), NOT the perl interpreter! If this parameter is empty, then CircosRender.DefaultCircosExe will be used.

method RemoveTicks #

RemoveTicks(Circos)

Removes the ticks label from the circos docuemnt node.

Parameters

Name	Type	Description
`doc`	Circos	-

method RemoveIdeogram #

RemoveIdeogram(Circos)

Removes the ideogram plots element from the circos document node.

Parameters

Name	Type	Description
`doc`	Circos	-

method Shell #

Shell(String, String)

Invoke the circos command line program for drawing the circos plots.

Parameters

Name Type Description

Name	Type	Description
`circos`	`String`	The file path of the circos executable program. NOTICE circos is a perl program, but on windows the perl interpreter is usually not installed. the official windows distribution provides a self-contained `bin\circos.exe` which already embeds the perl runtime, so this parameter should be the file path of that executable file, NOT the file path of the perl interpreter. If this parameter is empty, then the CircosRender.DefaultCircosExe will be used.
`conf`	`String`	The file path of the `circos.conf` file, by default is the `./circos.conf` file in the current working directory. Because circos uses a relative path to search for the data files, you should switch the terminal work directory to the directory which contains the circos.conf plots configuration file before invoke this method.

circos

String

The file path of the circos executable program.

NOTICE

circos is a perl program, but on windows the perl interpreter is usually not installed. the official windows distribution provides a self-contained bin\circos.exe which already embeds the perl runtime, so this parameter should be the file path of that executable file, NOT the file path of the perl interpreter.

If this parameter is empty, then the CircosRender.DefaultCircosExe will be used.

conf

String

The file path of the circos.conf file, by default is the ./circos.conf file in the current working directory.

Because circos uses a relative path to search for the data files, you should switch the terminal work directory to the directory which contains the circos.conf plots configuration file before invoke this method.

field null #

null

This property have no data value

field yes #

yes

field no #

field null #

null

method SetRadius #

SetRadius(Circos, Double, Double)