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Tiago Peixoto
graph-tool
Commits
124bbe06
Commit
124bbe06
authored
Sep 09, 2014
by
Tiago Peixoto
Browse files
Change default colormap
parent
9b147c0d
Changes
3
Hide whitespace changes
Inline
Side-by-side
src/graph_tool/centrality/__init__.py
View file @
124bbe06
...
...
@@ -138,6 +138,10 @@ def pagerank(g, damping=0.85, pers=None, weight=None, prop=None, epsilon=1e-6,
Examples
--------
.. testsetup:: pagerank
import matplotlib
.. doctest:: pagerank
>>> g = gt.collection.data["polblogs"]
...
...
@@ -145,7 +149,8 @@ def pagerank(g, damping=0.85, pers=None, weight=None, prop=None, epsilon=1e-6,
>>> pr = gt.pagerank(g)
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=pr,
... vertex_size=gt.prop_to_size(pr, mi=5, ma=15),
... vorder=pr, output="polblogs_pr.pdf")
... vorder=pr, vcmap=matplotlib.cm.gist_heat,
... output="polblogs_pr.pdf")
<...>
.. testcode:: pagerank
...
...
@@ -153,7 +158,8 @@ def pagerank(g, damping=0.85, pers=None, weight=None, prop=None, epsilon=1e-6,
gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=pr,
vertex_size=gt.prop_to_size(pr, mi=5, ma=15),
vorder=pr, output="polblogs_pr.png")
vorder=pr, vcmap=matplotlib.cm.gist_heat,
output="polblogs_pr.png")
.. figure:: polblogs_pr.*
...
...
@@ -172,7 +178,8 @@ def pagerank(g, damping=0.85, pers=None, weight=None, prop=None, epsilon=1e-6,
>>> pr = gt.pagerank(g, pers=p)
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=pr,
... vertex_size=gt.prop_to_size(pr, mi=5, ma=15),
... vorder=pr, output="polblogs_pr_pers.pdf")
... vorder=pr, vcmap=matplotlib.cm.gist_heat,
... output="polblogs_pr_pers.pdf")
<...>
.. testcode:: pagerank
...
...
@@ -180,6 +187,7 @@ def pagerank(g, damping=0.85, pers=None, weight=None, prop=None, epsilon=1e-6,
gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=pr,
vertex_size=gt.prop_to_size(pr, mi=5, ma=15),
vcmap=matplotlib.cm.gist_heat,
vorder=pr, output="polblogs_pr_pers.png")
...
...
@@ -275,6 +283,10 @@ def betweenness(g, vprop=None, eprop=None, weight=None, norm=True):
Examples
--------
.. testsetup:: betweenness
import matplotlib
.. doctest:: betweenness
>>> g = gt.collection.data["polblogs"]
...
...
@@ -283,6 +295,7 @@ def betweenness(g, vprop=None, eprop=None, weight=None, norm=True):
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=vp,
... vertex_size=gt.prop_to_size(vp, mi=5, ma=15),
... edge_pen_width=gt.prop_to_size(ep, mi=0.5, ma=5),
... vcmap=matplotlib.cm.gist_heat,
... vorder=vp, output="polblogs_betweenness.pdf")
<...>
...
...
@@ -292,6 +305,7 @@ def betweenness(g, vprop=None, eprop=None, weight=None, norm=True):
gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=vp,
vertex_size=gt.prop_to_size(vp, mi=5, ma=15),
edge_pen_width=gt.prop_to_size(ep, mi=0.5, ma=5),
vcmap=matplotlib.cm.gist_heat,
vorder=vp, output="polblogs_betweenness.png")
...
...
@@ -392,6 +406,10 @@ def closeness(g, weight=None, source=None, vprop=None, norm=True, harmonic=False
Examples
--------
.. testsetup:: closeness
import matplotlib
.. doctest:: closeness
>>> g = gt.collection.data["polblogs"]
...
...
@@ -399,6 +417,7 @@ def closeness(g, weight=None, source=None, vprop=None, norm=True, harmonic=False
>>> c = gt.closeness(g)
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=c,
... vertex_size=gt.prop_to_size(c, mi=5, ma=15),
... vcmap=matplotlib.cm.gist_heat,
... vorder=c, output="polblogs_closeness.pdf")
<...>
...
...
@@ -407,6 +426,7 @@ def closeness(g, weight=None, source=None, vprop=None, norm=True, harmonic=False
gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=c,
vertex_size=gt.prop_to_size(c, mi=5, ma=15),
vcmap=matplotlib.cm.gist_heat,
vorder=c, output="polblogs_closeness.png")
...
...
@@ -566,9 +586,11 @@ def eigenvector(g, weight=None, vprop=None, epsilon=1e-6, max_iter=None):
Examples
--------
.. testsetup:: eigenvector
np.random.seed(42)
import matplotlib
.. doctest:: eigenvector
...
...
@@ -581,6 +603,7 @@ def eigenvector(g, weight=None, vprop=None, epsilon=1e-6, max_iter=None):
729.229595705175
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=x,
... vertex_size=gt.prop_to_size(x, mi=5, ma=15),
... vcmap=matplotlib.cm.gist_heat,
... vorder=x, output="polblogs_eigenvector.pdf")
<...>
...
...
@@ -589,6 +612,7 @@ def eigenvector(g, weight=None, vprop=None, epsilon=1e-6, max_iter=None):
gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=x,
vertex_size=gt.prop_to_size(x, mi=5, ma=15),
vcmap=matplotlib.cm.gist_heat,
vorder=x, output="polblogs_eigenvector.png")
...
...
@@ -689,6 +713,7 @@ def katz(g, alpha=0.01, beta=None, weight=None, vprop=None, epsilon=1e-6,
.. testsetup:: katz
np.random.seed(42)
import matplotlib
.. doctest:: katz
...
...
@@ -699,6 +724,7 @@ def katz(g, alpha=0.01, beta=None, weight=None, vprop=None, epsilon=1e-6,
>>> x = gt.katz(g, weight=w)
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=x,
... vertex_size=gt.prop_to_size(x, mi=5, ma=15),
... vcmap=matplotlib.cm.gist_heat,
... vorder=x, output="polblogs_katz.pdf")
<...>
...
...
@@ -707,6 +733,7 @@ def katz(g, alpha=0.01, beta=None, weight=None, vprop=None, epsilon=1e-6,
gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=x,
vertex_size=gt.prop_to_size(x, mi=5, ma=15),
vcmap=matplotlib.cm.gist_heat,
vorder=x, output="polblogs_katz.png")
...
...
@@ -806,6 +833,10 @@ def hits(g, weight=None, xprop=None, yprop=None, epsilon=1e-6, max_iter=None):
Examples
--------
.. testsetup:: hits
import matplotlib
.. doctest:: hits
>>> g = gt.collection.data["polblogs"]
...
...
@@ -813,10 +844,12 @@ def hits(g, weight=None, xprop=None, yprop=None, epsilon=1e-6, max_iter=None):
>>> ee, x, y = gt.hits(g)
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=x,
... vertex_size=gt.prop_to_size(x, mi=5, ma=15),
... vcmap=matplotlib.cm.gist_heat,
... vorder=x, output="polblogs_hits_auths.pdf")
<...>
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=y,
... vertex_size=gt.prop_to_size(y, mi=5, ma=15),
... vcmap=matplotlib.cm.gist_heat,
... vorder=y, output="polblogs_hits_hubs.pdf")
<...>
...
...
@@ -825,20 +858,22 @@ def hits(g, weight=None, xprop=None, yprop=None, epsilon=1e-6, max_iter=None):
gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=x,
vertex_size=gt.prop_to_size(x, mi=5, ma=15),
vcmap=matplotlib.cm.gist_heat,
vorder=x, output="polblogs_hits_auths.png")
gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=y,
vertex_size=gt.prop_to_size(y, mi=5, ma=15),
vcmap=matplotlib.cm.gist_heat,
vorder=y, output="polblogs_hits_hubs.png")
.. figure:: polblogs_hits_auths.*
:align:
left
:align:
center
HITS authority values of the a political blogs network of
[adamic-polblogs]_.
.. figure:: polblogs_hits_hubs.*
:align:
right
:align:
center
HITS hub values of the a political blogs network of [adamic-polblogs]_.
...
...
@@ -928,6 +963,7 @@ def eigentrust(g, trust_map, vprop=None, norm=False, epsilon=1e-6, max_iter=0,
.. testsetup:: eigentrust
np.random.seed(42)
import matplotlib
.. doctest:: eigentrust
...
...
@@ -938,6 +974,7 @@ def eigentrust(g, trust_map, vprop=None, norm=False, epsilon=1e-6, max_iter=0,
>>> t = gt.eigentrust(g, w)
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=t,
... vertex_size=gt.prop_to_size(t, mi=5, ma=15),
... vcmap=matplotlib.cm.gist_heat,
... vorder=t, output="polblogs_eigentrust.pdf")
<...>
...
...
@@ -946,6 +983,7 @@ def eigentrust(g, trust_map, vprop=None, norm=False, epsilon=1e-6, max_iter=0,
gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=t,
vertex_size=gt.prop_to_size(t, mi=5, ma=15),
vcmap=matplotlib.cm.gist_heat,
vorder=t, output="polblogs_eigentrust.png")
...
...
@@ -1055,6 +1093,7 @@ def trust_transitivity(g, trust_map, source=None, target=None, vprop=None):
.. testsetup:: trust_transitivity
np.random.seed(42)
import matplotlib
.. doctest:: trust_transitivity
...
...
@@ -1068,6 +1107,7 @@ def trust_transitivity(g, trust_map, source=None, target=None, vprop=None):
>>> t = gt.trust_transitivity(g, w, source=g.vertex(42))
>>> gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=t,
... vertex_size=gt.prop_to_size(t, mi=5, ma=15),
... vcmap=matplotlib.cm.gist_heat,
... vorder=t, output="polblogs_trust_transitivity.pdf")
<...>
...
...
@@ -1076,6 +1116,7 @@ def trust_transitivity(g, trust_map, source=None, target=None, vprop=None):
gt.graph_draw(g, pos=g.vp["pos"], vertex_fill_color=t,
vertex_size=gt.prop_to_size(t, mi=5, ma=15),
vcmap=matplotlib.cm.gist_heat,
vorder=t, output="polblogs_trust_transitivity.png")
...
...
src/graph_tool/draw/__init__.py
View file @
124bbe06
...
...
@@ -81,11 +81,10 @@ from .. dl_import import dl_import
dl_import
(
"from . import libgraph_tool_layout"
)
__all__
=
[
"graph_draw"
,
"graphviz_draw"
,
"fruchterman_reingold_layout"
,
"arf_layout"
,
"sfdp_layout"
,
"random_layout"
,
"radial_tree_layout"
,
"cairo_draw"
,
"prop_to_size"
,
"get_hierarchy_control_points"
]
__all__
=
[
"graph_draw"
,
"graphviz_draw"
,
"fruchterman_reingold_layout"
,
"arf_layout"
,
"sfdp_layout"
,
"random_layout"
,
"radial_tree_layout"
,
"cairo_draw"
,
"prop_to_size"
,
"get_hierarchy_control_points"
,
"default_cm"
]
def
random_layout
(
g
,
shape
=
None
,
pos
=
None
,
dim
=
2
):
...
...
@@ -767,7 +766,7 @@ def radial_tree_layout(g, root, weighted=False, r=1.):
return
g
.
own_property
(
pos
)
try
:
from
.cairo_draw
import
graph_draw
,
cairo_draw
,
get_hierarchy_control_points
from
.cairo_draw
import
graph_draw
,
cairo_draw
,
get_hierarchy_control_points
,
default_cm
except
ImportError
:
pass
...
...
@@ -791,7 +790,7 @@ def prop_to_size(prop, mi=0, ma=5, log=False, power=0.5):
y = mi + (ma - mi) \left(\frac{x_i - min(x)} {max(x) - min(x)}\right)^\text{power}
If `log=True`, the natural logarithm of the property values
are
used instead.
If `log=True`, the natural logarithm of the property values
is
used instead.
"""
prop
=
prop
.
copy
(
value_type
=
"double"
)
...
...
src/graph_tool/draw/cairo_draw.py
View file @
124bbe06
...
...
@@ -34,6 +34,7 @@ except ImportError:
warnings
.
warn
(
msg
,
ImportWarning
)
raise
default_cm
=
None
try
:
import
matplotlib.cm
import
matplotlib.colors
...
...
@@ -297,14 +298,14 @@ def _convert(attr, val, cmap):
return
val
if
val
.
value_type
()
in
[
"int32_t"
,
"int64_t"
,
"double"
,
"long double"
,
"unsigned long"
,
"bool"
]:
if
val
.
fa
is
None
:
try
:
vrange
=
[
val
.
fa
.
min
(),
val
.
fa
.
max
()]
except
ValueError
:
vrange
=
val
[
val
.
get_graph
().
vertex
(
0
)]
vrange
=
[
vrange
,
vrange
]
for
v
in
val
.
get_graph
().
vertices
():
vrange
[
0
]
=
min
(
vrange
[
0
],
val
[
v
])
vrange
[
1
]
=
max
(
vrange
[
1
],
val
[
v
])
else
:
vrange
=
[
val
.
fa
.
min
(),
val
.
fa
.
max
()]
cnorm
=
matplotlib
.
colors
.
Normalize
(
vmin
=
vrange
[
0
],
vmax
=
vrange
[
1
])
if
val
.
key_type
()
==
"v"
:
...
...
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