nuget
api documents
circos.conf
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round Is good
circos - generate circularly composited information graphics(Circo基因组绘图程序的主配置文件)
00 Remarks
Typically a central configuration file which defines data track information (circos.conf) imports other configuration files that store parameters that change less frequently (tick marks, ideogram size, grid, etc).
Data for each data track Is stored in a file And the same file can be used for multiple tracks.
01 Syntax
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| .ctor | 1 | Creates a new empty circos document. |
| NormalizeDirectory | 1 | 将输入的文件夹路径统一转换为使用/作为分隔符的相对路径或者绝对路径 |
| mkdir | 1 | 创建指定文件所在的文件夹（如果文件夹不存在的话） |
| trimRelative | 1 | ./data/genome_skeleton.txt --> data/genome_skeleton.txt |
| CreateObject | 1 | Creates a new circos document with the default distributed includes (colors_fonts_patterns / housekeeping / image). |
| AddTrack | 1 | 函数会根据元素的个数的情况自动的调整在圈内的位置 |
| ForceAutoLayout | 2 | 强制所有的元素都自动布局 |
| TracksInBlock | 1 | 取出归属于指定的顶层配置块之中的所有的绘图元素 |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| karyotype | 1 | The basically genome structure plots: Chromosome name, size and color definition.(基本的数据文件) |
| chromosomes_units | 1 | The chromosomes_unit value is used as a unit (suffix "u") to shorten values In other parts Of the configuration file. |
| chromosomes_display_default | 1 | The default behaviour is to display all chromosomes defined in the karyotype file. |
| chromosomes_reverse | 1 | By default, the scale progression is clockwise. |
| chromosomes_radius | 1 | The default radial position for all ideograms is set by 'radius' in the <ideogram> block (see ideogram.conf). |
| chromosomes_scale | 1 | The size of the ideogram on the figure can be adjusted using an absolute Or relative magnification. |
| chromosomes_color | 1 | The color of each ideogram is taken from the karyotype file. |
| skeletonKaryotype | 1 | 基因组的骨架信息 |
| GdiPlusImageSize | 1 | 内置 GDI+ 绘图引擎所使用的画布尺寸。 这个属性没有使用 CircosAttribute 标记，所以它不会被序列化到 circos.conf 配置文件之中（不会影响到命令行调用 circos 的既有流程）， 仅用于 GdiPlus.GdiRender 在没有显式指定渲染参数的时候确定输出图像的尺寸。 |
| GdiPlusDpi | 1 | 内置 GDI+ 绘图引擎所使用的 DPI（同样不会参与 circos.conf 的序列化输出，仅用于 GdiPlus.GdiRender） |
| Ideogram | 1 | 获取到被包含在主配置文件之中的 ideogram 配置块 |
| size | 1 | The genome size.(基因组的大小，当Circos.skeletonKaryotype为空值的时候返回数值0) |
| Plots | 1 | 内部元素是有顺序的区别的 |
| numberOfTracks | 1 | Gets the number of the tracks that defined in this circos model |
04 Members
Creates a new empty circos document.
在旧的实现之中只有 Circos.CreateObject() 会初始化 CircosConfig.includes 列表， 直接使用 New Circos() 所创建出来的对象的 CircosConfig.includes 是 Nothing， 后续调用 circos.includes.Add 会直接抛出 NullReferenceException， 所以在这里将初始化逻辑移动到构造函数之中
String)将输入的文件夹路径统一转换为使用/作为分隔符的相对路径或者绝对路径
在旧的代码实现之中直接使用传入的directory参数拼接子路径， 当调用方不传入任何参数的时候会拼出类似于/data/xxxx.txt这样的非法路径
| Name | Type | Description |
|---|---|---|
directory$ | String | - |
String)创建指定文件所在的文件夹（如果文件夹不存在的话）
| Name | Type | Description |
|---|---|---|
file$ | String | - |
String)./data/genome_skeleton.txt --> data/genome_skeleton.txt
| Name | Type | Description |
|---|---|---|
url$ | String | - |
Creates a new circos document with the default distributed includes (colors_fonts_patterns / housekeeping / image).
Boolean)函数会根据元素的个数的情况自动的调整在圈内的位置
| Name | Type | Description |
|---|---|---|
track | ITrackPlot | - |
强制所有的元素都自动布局
强制所指定的绘图元素自动布局
| Name | Type | Description |
|---|---|---|
tracks | ITrackPlot() | - |
String)取出归属于指定的顶层配置块之中的所有的绘图元素
| Name | Type | Description |
|---|---|---|
blockName | String | 仅可以为 CircosBlocks.plots、CircosBlocks.links 或者 CircosBlocks.highlights |
The basically genome structure plots: Chromosome name, size and color definition.(基本的数据文件)
The chromosomes_unit value is used as a unit (suffix "u") to shorten values In other parts Of the configuration file. Some parameters, such As ideogram And tick spacing, accept "u" suffixes, so instead Of
spacing = 10000000you can write
spacing = 10uThe default behaviour is to display all chromosomes defined in the karyotype file. In this example, I Select only a subset.
The 'chromosomes' parameter has several uses, and selecting which chromosomes To show Is one Of them. You can list them
hs1;hs2;hs3;hs4Or provide a regular expression that selects them based On a successful match
/hs[1-4]$/The $ anchor Is necessary, otherwise chromosomes Like hs10, hs11 And hs20 are also matched.
By default, the scale progression is clockwise. You can set the Global angle progression Using 'angle_orientation' in the <image> block (clockwise Or counterclockwise). To reverse it For one Or several ideograms, use 'chromosomes-reverse'
The default radial position for all ideograms is set by 'radius' in the <ideogram> block (see ideogram.conf). To change the value For specific ideograms, use chromosomes_radius.
The size of the ideogram on the figure can be adjusted using an absolute Or relative magnification. Absolute scaling,
hs1=0.5shrinks Or expands the ideogram by a fixed factor. When the "r" suffix Is used, the magnification becomes relative To the circumference Of the figure. Thus,
hs1=0.5rmakes hs1 To occupy 50% Of the figure. To uniformly distribute several ideogram within a fraction Of the figure, use a regular expression that selects the ideograms And the "rn" suffix (relative normalized).
/hs[234]/=0.5RnWill match hs2, hs3, hs4 And divide them evenly into 50% Of the figure. Each ideogram will be about 16% Of the figure.
The color of each ideogram is taken from the karyotype file. To change it, use 'chromosomes_color'.
基因组的骨架信息
内置 GDI+ 绘图引擎所使用的画布尺寸。
这个属性没有使用 CircosAttribute 标记，所以它不会被序列化到 circos.conf 配置文件之中（不会影响到命令行调用 circos 的既有流程）， 仅用于 GdiPlus.GdiRender 在没有显式指定渲染参数的时候确定输出图像的尺寸。
内置 GDI+ 绘图引擎所使用的 DPI（同样不会参与 circos.conf 的序列化输出，仅用于 GdiPlus.GdiRender）
获取到被包含在主配置文件之中的 ideogram 配置块
当主配置文件之中并没有包含 ideogram 配置的时候返回 Nothing
The genome size.(基因组的大小，当Circos.skeletonKaryotype为空值的时候返回数值0)
内部元素是有顺序的区别的
Gets the number of the tracks that defined in this circos model