load_attributes[source]

load_attributes(yaml_file)

Load the self-defined attributes from a yaml file

test load_attributes

attrs=load_attributes('data/default.yaml')

attrs

{'trait1': {'fillcolor': {1: 'white', 2: 'dimgrey', -9: 'aquamarine3'}},
 'trait2': {'style': {True: 'filled,setlinewidth(4)', False: 'filled'}},
 'trait3': {'fontcolor': {True: 'darkorange', False: 'black'}}}

readped[source]

readped(file, attrs=None)

the number of traits in the input file should match with the number of traits in the attribute yaml file

test readped

fam=readped('data/example_fam.ped')
fam

	fid	iid	fathid	mothid	sex	trait
0	Fam	F4	P3	F1	1	1
1	Fam	F3	P3	F1	2	1
2	Fam	F2	P3	F1	2	1
3	Fam	F1	P1	P2	2	2
4	Fam	P3	0	0	1	2
5	Fam	P1	0	0	1	-9
6	Fam	P2	0	0	2	-9

attrs=load_attributes('data/default.yaml')
famext=readped('data/example_fam_ext.ped',attrs)
famext

	fid	iid	fathid	mothid	sex	trait1	trait2	trait3
0	Fam1	F4	P3	F1	1	1	True	False
1	Fam1	F3	P3	F1	2	1	True	True
2	Fam1	F2	P3	F1	2	1	True	False
3	Fam1	F1	P1	P2	2	2	True	False
4	Fam1	P3	0	0	1	2	True	False
5	Fam1	P1	0	0	1	-9	False	True
6	Fam1	P2	0	0	2	-9	False	True

update_attributes[source]

update_attributes(r, attrs=None)

Assign each node specific attributes

plotped[source]

plotped(fi, attrs=None, output=None, format='svg', engine='dot')

The core function of pedigree drawing

test plotped

dot = Digraph()

a=plotped(fam)
a

plotped(famext,attrs)

get_args[source]

get_args()

The arguments of graphped

test get_args

args = get_args().parse_args('-p data/fam.ped -f svg'.split())

args

Namespace(ped='data/fam.ped', output='./', format='svg', attributes=None, engine='dot')

GraphPedCli[source]

GraphPedCli()

The command line function of GraphPed

GraphPed[source]

GraphPed(ped, attrs=None, output=None, format='svg', engine='dot')

Draw pedigree plot from ped

test GraphPed

dots=GraphPed(fam)
dots[0]

GraphPed(famext,attrs)[0]

show[source]

show(dot)

Plot a pedigree of a list of pedigrees in Jupyter Notebook

test show

show(dots)