Functions | |
def | rmuller_spy_matrix_pil |
def | rmuller_pcolor_matrix_pil |
def | rmuller_get_color |
def | draw_pedigree |
def | plot_founders_by_year |
def | plot_founders_pct_by_year |
def | pcolor_matrix_pylab |
def | spy_matrix_pylab |
def | plot_line_xy |
def | new_draw_pedigree |
def PyPedal::pyp_graphics::draw_pedigree | ( | pedobj, | ||
gfilename = 'pedigree' , |
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gtitle = '' , |
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gformat = 'jpg' , |
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gsize = 'f' , |
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gdot = '1' , |
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gorient = 'p' , |
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gdirec = '' , |
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gname = 0 , |
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gfontsize = 10 , |
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garrow = 1 , |
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gtitloc = 'b' , |
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gtitjust = 'c' , |
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gshowall = 1 , |
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gclusters = 0 | ||||
) |
draw_pedigree() uses the pydot bindings to the graphviz library -- if they are available on your system -- to produce a directed graph of your pedigree with paths of inheritance as edges and animals as nodes. If there is more than one generation in the pedigree as determind by the "gen" attributes of the animals in the pedigree, draw_pedigree() will use subgraphs to try and group animals in the same generation together in the drawing.
pedobj | A PyPedal pedigree object. | |
gfilename | The name of the file to which the pedigree should be drawn | |
gtitle | The title of the graph. | |
gformat | The format in which the output file should be written (JPG|PNG|PS). | |
gsize | The size of the graph: 'f': full-size, 'l': letter-sized page. | |
gdot | Whether or not to write the dot code for the pedigree graph to a file (can produce large files). | |
gorient | The orientation of the graph: 'p': portrait, 'l': landscape. | |
gdirec | Direction of flow from parents to offspring: 'TB': top-bottom, 'LR': left-right, 'RL': right-left. | |
gname | Flag indicating whether ID numbers (0) or names (1) should be used to label nodes. | |
gfontsize | Integer indicating the typeface size to be used in labelling nodes. | |
garrow | Flag indicating whether or not arrowheads should be drawn. | |
gtitloc | Indicates if the title be drawn or above ('t') or below ('b') the graph. | |
gtitjust | Indicates if the title should be center- ('c'), left- ('l'), or right-justified ('r'). | |
gshowall | Draws animals with no links to other ancestors in the pedigree (1) or suppresses them (0). |
draw_pedigree() uses the pydot bindings to the graphviz library -- if they are available on your system -- to produce a directed graph of your pedigree with paths of inheritance as edges and animals as nodes. If there is more than one generation in the pedigree as determind by the "gen" attributes of the animals in the pedigree, draw_pedigree() will use subgraphs to try and group animals in the same generation together in the drawing.
Definition at line 247 of file pyp_graphics.py.
def PyPedal::pyp_graphics::new_draw_pedigree | ( | pedobj, | ||
gfilename = 'pedigree' , |
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gtitle = '' , |
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gformat = 'jpg' , |
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gsize = 'f' , |
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gdot = 1 , |
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gorient = 'p' , |
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gdirec = '' , |
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gname = 0 , |
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garrow = 1 , |
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gtitloc = 'b' , |
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gtitjust = 'c' , |
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gshowall = 1 , |
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gprog = 'dot' | ||||
) |
new_draw_pedigree() uses the pyygraphviz to produce a directed graph of your pedigree with paths of inheritance as edges and animals as nodes. If there is more than one generation in the pedigree as determind by the "gen" attributes of the animals in the pedigree, draw_pedigree() will use subgraphs to try and group animals in the same generation together in the drawing.
pedobj | A PyPedal pedigree object. | |
gfilename | The name of the file to which the pedigree should be drawn | |
gtitle | The title of the graph. | |
gformat | The format in which the output file should be written (JPG|PNG|PS). | |
gsize | The size of the graph: 'f': full-size, 'l': letter-sized page. | |
gdot | Whether or not to write the dot code for the pedigree graph to a file (can produce large files). | |
gorient | The orientation of the graph: 'p': portrait, 'l': landscape. | |
gdirec | Direction of flow from parents to offspring: 'TB': top-bottom, 'LR': left-right, 'RL': right-left. | |
gname | Flag indicating whether ID numbers (0) or names (1) should be used to label nodes. | |
garrow | Flag indicating whether or not arrowheads should be drawn. | |
gtitloc | Indicates if the title be drawn or above ('t') or below ('b') the graph. | |
gtitjust | Indicates if the title should be center- ('c'), left- ('l'), or right-justified ('r'). | |
gshowall | Draws animals with no links to other ancestors in the pedigree (1) or suppresses them (0). | |
gprog | Specify which program should be used to position and render the graph. |
draw_pedigree() uses the pydot bindings to the graphviz library -- if they are available on your system -- to produce a directed graph of your pedigree with paths of inheritance as edges and animals as nodes. If there is more than one generation in the pedigree as determind by the "gen" attributes of the animals in the pedigree, draw_pedigree() will use subgraphs to try and group animals in the same generation together in the drawing.
Definition at line 757 of file pyp_graphics.py.
def PyPedal::pyp_graphics::pcolor_matrix_pylab | ( | A, | ||
fname = 'pcolor_matrix_matplotlib' | ||||
) |
pcolor_matrix_pylab() implements a matlab-like 'pcolor' function to display the large elements of a matrix in pseudocolor using the Python Imaging Library.
A | Input Numpy matrix (such as a numerator relationship matrix). | |
fname | Output filename to which to dump the graphics (default 'tmp.png') | |
do_outline | Whether or not to print an outline around the block (default 0) | |
height | The height of the image (default 300) | |
width | The width of the image (default 300) |
pcolor_matrix_pylab() implements a matlab-like 'pcolor' function to display the large elements of a matrix in pseudocolor using the Python Imaging Library.
Definition at line 604 of file pyp_graphics.py.
def PyPedal::pyp_graphics::plot_founders_by_year | ( | pedobj, | ||
gfilename = 'founders_by_year' , |
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gtitle = 'Founders by Birthyear' | ||||
) |
founders_by_year() uses matplotlib -- if available on your system -- to produce a bar graph of the number (count) of founders in each birthyear.
pedobj | A PyPedal pedigree object. | |
gfilename | The name of the file to which the pedigree should be drawn | |
gtitle | The title of the graph. |
founders_by_year() uses matplotlib -- if available on your system -- to produce a bar graph of the number (count) of founders in each birthyear.
Definition at line 509 of file pyp_graphics.py.
def PyPedal::pyp_graphics::plot_founders_pct_by_year | ( | pedobj, | ||
gfilename = 'founders_pct_by_year' , |
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gtitle = 'Founders by Birthyear' | ||||
) |
founders_pct_by_year() uses matplotlib -- if available on your system -- to produce a line graph of the frequency (percentage) of founders in each birthyear.
pedobj | A PyPedal pedigree object. | |
gfilename | The name of the file to which the pedigree should be drawn | |
gtitle | The title of the graph. |
founders_pct_by_year() uses matplotlib -- if available on your system -- to produce a line graph of the frequency (percentage) of founders in each birthyear.
Definition at line 554 of file pyp_graphics.py.
def PyPedal::pyp_graphics::plot_line_xy | ( | xydict, | ||
gfilename = 'plot_line_xy' , |
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gtitle = 'Value by key' , |
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gxlabel = 'X' , |
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gylabel = 'Y' , |
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gformat = 'png' | ||||
) |
plot_line_xy() uses matplotlib -- if available on your system -- to produce a line graph of the values in a dictionary for each level of key.
dictionary | A Python dictionary | |
gfilename | The name of the file to which the figure should be written | |
gtitle | The title of the graph. | |
gxlabel | The label for the x-axis. | |
gylabel | The label for the y-axis. |
plot_line_xy() uses matplotlib -- if available on your system -- to produce a line graph of the values in a dictionary for each level of key.
Definition at line 699 of file pyp_graphics.py.
def PyPedal::pyp_graphics::rmuller_get_color | ( | a, | ||
cmin, | ||||
cmax | ||||
) |
rmuller_get_color() Converts a float value to one of a continuous range of colors using recipe 9.10 from the Python Cookbook.
a | Float value to convert to a color. | |
cmin | Minimum value in array (?). | |
cmax | Maximum value in array (?). |
Convert a float value to one of a continuous range of colors. Rewritten to use recipe 9.10 from the O'Reilly Python Cookbook.
Definition at line 210 of file pyp_graphics.py.
def PyPedal::pyp_graphics::rmuller_pcolor_matrix_pil | ( | A, | ||
fname = 'tmp.png' , |
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do_outline = 0 , |
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height = 300 , |
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width = 300 | ||||
) |
rmuller_pcolor_matrix_pil() implements a matlab-like 'pcolor' function to display the large elements of a matrix in pseudocolor using the Python Imaging Library.
A | Input Numpy matrix (such as a numerator relationship matrix). | |
fname | Output filename to which to dump the graphics (default 'tmp.png') | |
do_outline | Whether or not to print an outline around the block (default 0) | |
height | The height of the image (default 300) | |
width | The width of the image (default 300) |
rmuller_pcolor_matrix_pil() implements a matlab-like 'pcolor' function to display the large elements of a matrix in pseudocolor using the Python Imaging Library.
Definition at line 142 of file pyp_graphics.py.
def PyPedal::pyp_graphics::rmuller_spy_matrix_pil | ( | A, | ||
fname = 'tmp.png' , |
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cutoff = 0.1 , |
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do_outline = 0 , |
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height = 300 , |
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width = 300 | ||||
) |
import matplotlib matplotlib.use('Agg') import pylab rmuller_spy_matrix_pil() implements a matlab-like 'spy' function to display the sparsity of a matrix using the Python Imaging Library.
A | Input Numpy matrix (such as a numerator relationship matrix). | |
fname | Output filename to which to dump the graphics (default 'tmp.png') | |
cutoff | Threshold value for printing an element (default 0.1) | |
do_outline | Whether or not to print an outline around the block (default 0) | |
height | The height of the image (default 300) | |
width | The width of the image (default 300) |
rmuller_spy_matrix_pil() implements a matlab-like 'spy' function to display the sparsity of a matrix using the Python Imaging Library.
Definition at line 82 of file pyp_graphics.py.
def PyPedal::pyp_graphics::spy_matrix_pylab | ( | A, | ||
fname = 'spy_matrix_matplotlib' | ||||
) |
spy_matrix_pylab() implements a matlab-like 'pcolor' function to display the large elements of a matrix in pseudocolor using the Python Imaging Library.
A | Input Numpy matrix (such as a numerator relationship matrix). | |
fname | Output filename to which to dump the graphics (default 'tmp.png') | |
do_outline | Whether or not to print an outline around the block (default 0) | |
height | The height of the image (default 300) | |
width | The width of the image (default 300) |
spy_matrix_pylab() implements a matlab-like 'pcolor' function to display the large elements of a matrix in pseudocolor using the Python Imaging Library.
Definition at line 658 of file pyp_graphics.py.