API Docs / SMRUCC.genomics.Visualize.Circos.Core 1.0.9753.40023 1.0.9762.7562
SMRUCC.genomics.Visualize.Circos.Core 1.0.9753.40023 .
Namespaces 15
Types 83
Members 548
01 Namespaces
SMRUCC.genomics.Visualize.Circos
SMRUCC.genomics.Visualize.Circos.Colors
SMRUCC.genomics.Visualize.Circos.Configurations
Type Summary
Members
Circos circos.conf _ / _(_)_ _ _ _ | | | | '/ / _ \/ |…
46
CircosAttribute Alias for SimpleConfig
0
CircosRender Invoke the circos command line tools for drawing the circos plot.
8
CircosRenderResult The result package of a circos rendering invocation.
9
Extensions 9
IdeogramInclude The <ideogram> block defines the position, size, labels and other properties Of the segments On which data are drawn.
1
SMRUCC.genomics.Visualize.Circos.Configurations.ComponentModel
Type Summary
Members
CircosBlocks The circos allowed top level configuration block names.
6
CircosConfig Abstract of the circos config files.
12
CircosDistributed The circos distributed includes files.
6
ICircosDocNode This object can be convert to text document by using method ICircosDocNode.Build())
1
ICircosDocument This object can be save as a text doc for the circos plot
0
OverwritesColors Use Circos.chromosomes_color to change the color Of the ideograms.
2
SMRUCC.genomics.Visualize.Circos.Configurations.Nodes
SMRUCC.genomics.Visualize.Circos.Configurations.Nodes.Plots
Type Summary
Members
ConditionalRule Rules are used to dynamically alter the format of a data point, based on the value of the data point (or any other property of it).
14
Connector 可以用来表示调控关系
2
HeatMap Heat maps are used for data types which associate a value with a genomic position, Or region.
4
Highlight 5
Histogram Histograms are a type Of track that displays 2D data, which associates a value With a genomic position.
3
ITrackPlot Abstract model of the tracks plot
15
LinkPlot Links are defined in <link> blocks enclosed in a <links> block.
9
LinksBlock The <links> top level block helper.(用于生成 circos 配置文件之中的顶层 <links> 块)
1
ScatterPlot Scatter plots are useful for showing the position of a probe, such as SNP data, on the genome.
5
TextLabel Like with other tracks, text is limited to a radial range by setting r0 And r1.
18
TilePlot Tile tracks are the Circos equivalent of a genome browser.
6
TrackPlot 25
SMRUCC.genomics.Visualize.Circos.Configurations.Nodes.Plots.Lines
Type Summary
Members
LinePlot Line plots are useful for showing values associated with a position on the ideogram, such as sequence conservation scores, or values derived from a sliding window scan of the gen…
3
SMRUCC.genomics.Visualize.Circos.GdiPlus
Type Summary
Members
ChromosomeBand 一条染色体（ideogram 区段）在圆环之上的角度布局信息
7
CircosColorResolver 将 circos/perl 的颜色表达式解析为 .NET 的 Color 对象。 现有的 CircosColor.FromKnownColorName()) 无法解析 circos 发行版之中的 间接颜色定义（例如 vdgrey = greys-9-seq-7）以及带透明度的颜色名 （例如 red_a2 / black_a4），会导致大量颜色退化为…
4
CircosLayout circos 文档对象到圆环几何（角度/半径）的映射。 负责： + 按染色体的长度与 ideogram.spacing 分配角度区间 + 处理单染色体模型之中的 loopHole 缺口 + 将基因组坐标映射为角度
9
CircosUnits circos 配置之中 r / p / u 等尺寸单位的解析与换算工具。 + r：相对于图像半径的比例值（例如 0.85r） + p：绝对像素值（例如 25p） + u：相对于 chromosomes_units 的基因组坐标单位（例如 1u） + dims(...)：引用图像/ideogram 的尺寸表达式（例如 dims(ideogram,r…
7
GdiCanvas 封装 IGraphics，提供圆环绘图所需的高层几何辅助方法。 角度约定：0 度为正上方（12 点钟方向），顺时针方向为正。 （GDI+ 自身以 3 点钟方向为 0 度、顺时针为正，内部会自动做 -90 度的换算）
16
GdiRender 内置 GDI+ 绘图引擎的渲染入口。 直接读取已经构建完成的 circos 文档对象（Circos），在 .NET 环境 之中通过 GDI+ 绘制出圆环图并输出 PNG 图像，整个过程不需要依赖外部安装的 circos 程序。
2
GdiRenderContext 内置 GDI+ 绘图引擎的渲染上下文。 持有绘图设备、几何布局以及文档对象，并为各个渲染器提供统一的颜色/半径换算入口。
14
GdiRenderOptions 内置 GDI+ 绘图引擎的画布参数。 取值优先级为：渲染参数（GdiRenderOptions.ApplyOverrides())） > 文档配置（Circos.GdiPlusImageSize） > 默认值。
12
SMRUCC.genomics.Visualize.Circos.GdiPlus.Tracks
Type Summary
Members
IdeogramRenderer 基因组骨架圈（ideogram / cytogenetic bands / 标签）与刻度（ticks）的绘制
4
LinkRenderer 顶层 <links> 块（染色体区段之间的贝塞尔连线/缎带）的绘制
3
PlotsRenderer 各类 2D 绘图轨道（histogram / heatmap / line / scatter / tile / connector / text / highlight） 以及 <rules>、<axes>、<backgrounds> 子块的绘制。
4
RuleEvaluator circos <rule> 的 condition 表达式求值。 支持形如 var(value) > 0.6、var(value) <= -0.1 的简单比较表达式。
1
TrackGeometry 轨道（track）的径向几何换算：把数据值映射为画布半径。 + orientation = out：数据从内圈（r0）向外圈（r1）生长 + orientation = in：数据从外圈（r1）向内圈（r0）生长
10
SMRUCC.genomics.Visualize.Circos.GdiPlus.Tracks.IdeogramRenderer
SMRUCC.genomics.Visualize.Circos.Karyotype
Type Summary
Members
Band Bands are defined using band CHRNAME BANDNAME BANDLABEL START End COLOR Currently BANDNAME And BANDLABEL are Not used Colors correspond To levels Of grey To match conven…
8
ChromosomeGenerator 1
DOOROperon 最外层的Ideogram，
1
GenomeKaryotype The very basically genome skeleton information description.(基因组的基本框架的描述信息)
3
KaryotypeEntry The ideogram using karyotype file to define the genome skeleton information, which defines the name, size and color of chromosomes.
7
KaryotypeExtensions 1
KaryotypeSkeleton The annotated genome skeleton information.
8
SMRUCC.genomics.Visualize.Circos.Karyotype.GeneObjects
SMRUCC.genomics.Visualize.Circos.TrackDatas
Type Summary
Members
ConnectorDocument The connector plot data document: chr start end, the connector track does not take a value, only a genomic region.
0
Extensions 3
FeatureAnnotations 5
Formatting Annotated with formatting parameters that control how the point Is drawn.
17
ITrackData 通常是使用Object方法来生成数据文件之中的行数据的
2
LinkData + Finally, links are a special track type which associates two ranges together.
5
RegionTrackData 这个只是用来表示基因组上面的一个区域位置
0
StackedTrackData The exception Is a stacked histogram, which associates a list Of values With a range.
1
TextTrackData The value For a text track Is interpreted As a text label (other tracks require that this field be a floating point number).
1
TrackData Data for tracks is loaded from a plain-text file.
6
TrackDataDocument Tracks data document generator.(使用这个对象生成data文件夹之中的数据文本文件)
5
ValueTrackData Tracks such As scatter plot, line plot, histogram Or heat map, associate a value With Each range.
1
SMRUCC.genomics.Visualize.Circos.TrackDatas.Highlights
SMRUCC.genomics.Visualize.Circos.TrackDatas.NtProps
nuget