Package Bio :: Package Graphics :: Package GenomeDiagram :: Module _Graph :: Class GraphData
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Class GraphData

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object --+
         |
        GraphData

GraphData

Provides:

Methods:

o __init__(self, id=None, data=None, name=None, style='bar',
         color=colors.lightgreen, altcolor=colors.darkseagreen)
         Called on instantiation

o set_data(self, data)  Load the object with data to be plotted

o get_data(self)    Returns the data to be plotted as a list of
                    (position, value) tuples

o add_point(self, point)    Add a single point to the data set

o quartiles(self)   Returns a tuple of the data quartiles

o range(self)   Returns a tuple of the base range covered by the graph
                data

o mean(self)    Returns a float of the mean data point value

o stdev(self)   Returns the sample standard deviation of the data values

o __len__(self) Returns the length of sequence covered by the data

o __getitem__(self, index)  Returns the value at the base specified,
                            or graph data in the base range

o __str__(self) Returns a formatted string describing the graph data

Attributes:

o id    Unique identifier for the data

o data  Dictionary of describing the data, keyed by position

o name  String describing the data

o style String ('bar', 'heat', 'line') describing how to draw the data

o poscolor     colors.Color for drawing high (some styles) or all
                values

o negcolor     colors.Color for drawing low values (some styles)

o linewidth     Int, thickness to draw the line in 'line' styles

Instance Methods [hide private]
 
__init__(self, id=None, data=None, name=None, style='bar', color=colors.lightgreen, altcolor=colors.darkseagreen)
o id Unique ID for the graph
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set_data(self, data)
o data List of (position, value) tuples
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[(int, float), (int, float), ...]

get_data(self)
Return data as a list of sorted (position, value) tuples
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add_point(self, point)
o point (position, value) tuple
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(float, float, float, float, float)

quartiles(self)
Returns the (minimum, lowerQ, medianQ, upperQ, maximum) values as...
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(int, int)

range(self)
Returns the range of the data, i.e.
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Float

mean(self)
Returns the mean value for the data points
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Float

stdev(self)
Returns the sample standard deviation for the data
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Int

__len__(self)
Returns the number of points in the data set
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Float or list of tuples

__getitem__(self, index)
Given an integer representing position on the sequence returns a float - the data value at the passed position.
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""

__str__(self)
Returns a string describing the graph data
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, id=None, data=None, name=None, style='bar', color=colors.lightgreen, altcolor=colors.darkseagreen)
(Constructor)

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o id    Unique ID for the graph

o data  List of (position, value) tuples

o name  String describing the graph

o style String describing the presentation style ('bar', 'line',
        'heat')

o color   colors.Color describing the color to draw all or the
          'high' (some styles) values (overridden by backwards
          compatible argument with UK spelling, colour).

o altcolor colors.Color describing the color to draw the 'low'
           values (some styles only) (overridden by backwards
           compatible argument with UK spelling, colour).

o center Value at which x-axis crosses y-axis.

Overrides: object.__init__

set_data(self, data)

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o data      List of (position, value) tuples

Add data with a list of (position, value) tuples

add_point(self, point)

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o point     (position, value) tuple

Add a single point to the set of data

quartiles(self)

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Returns the (minimum, lowerQ, medianQ, upperQ, maximum) values as
a tuple

Returns:
(float, float, float, float, float)

range(self)

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Returns the range of the data, i.e. its start and end points on
the genome as a (start, end) tuple

Returns:
(int, int)

__getitem__(self, index)
(Indexing operator)

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Given an integer representing position on the sequence
returns a float - the data value at the passed position.

If a slice, returns graph data from the region as a list or
(position, value) tuples. Slices with step are not supported.

Returns the data value at the passed position

Returns:
Float or list of tuples

__str__(self)
(Informal representation operator)

source code 
Returns a string describing the graph data

Returns:
""

Overrides: object.__str__