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 a tuple
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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

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)

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Returns a string describing the graph data
Returns: ""
Overrides: object.__str__