TrackData

namespace: SMRUCC.genomics.Visualize.Circos.TrackDatas

Data for tracks is loaded from a plain-text file. Each data point is stored on a
separate line, except for links which use two lines per link.

The definition Of a data point within a track Is based On the genomic range,
which Is a combination Of chromosome And start/End position.

Data for tracks is loaded from a plain-text file. Each data point is stored on a separate line, except for links which use two lines per link.
The definition Of a data point within a track Is based On the genomic range, which Is a combination Of chromosome And start/End position.
For example,

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>  # the basis for a data point Is a range
> chr12 1000 5000
>

All data values, regardless Of track type, will be positioned Using a range rather than a Single position. To explicitly specify a Single position,
use a range With equal start And End positions.

  • Tracks such As scatter plot, line plot, histogram Or heat map, associate a value With Each range. The input To this kind Of track would be

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    >  # scatter, line, histogram And heat maps require a value
    > chr12 1000 5000 0.25
    >
  • The exception Is a stacked histogram, which associates a list Of values With a range.

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    >  # stacked histograms take a list of values
    > chr12 1000 5000 0.25,0.35,0.60
    >
  • The value For a text track Is interpreted As a text label (other tracks require that this field be a floating point number).

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    >  # value for text tracks Is interpreted as text
    > chr12 1000 5000 geneA
    >
  • The tile track does Not take a value—only a range.

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    >  chr12 1000 5000
    >
  • Finally, links are a special track type which associates two ranges together. The format For links Is analogous To other data types,
    except now two coordinates are specified.

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    >  chr12 1000 5000 chr15 5000 7000
    >
  • In addition to the chromosome, range And (if applicable) value, each data point can be annotated with formatting parameters that control how the point Is drawn.
    The parameters need to be compatible with the track type for which the file Is destined. Thus, a scatter plot data point might have

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    >  chr12 1000 5000 0.25 glyph_size=10p,glyph=circle
    >

whereas a histogram data point might include the Option To fill the data value’s bin

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>  chr12 1000 5000 0.25 fill_color=orange
>
  • Other features, such As URLs, can be associated With any data point. For URLs the parameter can contain parsable fields (e.g. [start]) which
    are populated automatically With the data point’s associated property.

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    >  # the URL for this point would be
    > # http://domain.com/script?start=1000&end=5000&chr=chr12
    > chr12 1000 5000 0.25 url=http//domain.com/script?start=[start]&end=[end]&chr=[chr]
    >

Methods

ToString

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SMRUCC.genomics.Visualize.Circos.TrackDatas.TrackData.ToString

Using @”M:SMRUCC.genomics.Visualize.Circos.TrackDatas.TrackData.ToString” method for creates tracks data document.

Properties

chr

Chromosomes name