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Changes to DAG plot.

This commit is contained in:
Einar Ryeng 2009-02-06 22:21:51 +00:00
parent 5cfa505ae2
commit f07ce85e46
2 changed files with 14 additions and 9 deletions
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21
workflows/gobrowser.py
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@ -483,8 +483,9 @@ class SetICFunction(workflow.Function):
return
class PlotDagFunction(workflow.Function):
def __init__(self):
def __init__(self, subtree="bp"):
workflow.Function.__init__(self, 'go-dag', 'Build DAG')
self.subtree = subtree
def run(self, selection):
g = self.get_network(list(selection['go-terms']))
@ -493,7 +494,7 @@ class PlotDagFunction(workflow.Function):
name="DAG")
return [ThresholdDagPlot(g)]
def get_network(self, terms, subtree='bp'):
def get_network(self, terms):
"""Returns a DAG connecting the given terms by including their parents
up to the level needed to connect them. The subtree parameter is one of
mf - molecular function
@ -502,6 +503,7 @@ class PlotDagFunction(workflow.Function):
rpy.r.library("GOstats")
subtree = self.subtree
if subtree == 'mf':
subtree_r = rpy.r.GOMFPARENTS
elif subtree == 'bp':
@ -573,6 +575,7 @@ class DagPlot(plots.Plot):
self._nodecolor = nodecolor
self._with_labels = with_labels
self.visible = set()
self.labels = {}
self.current_dim = dim
@ -753,15 +756,15 @@ class ThresholdDagPlot(DagPlot, plots.PlotThresholder):
with_labels=False, name='DAG Plot'):
DagPlot.__init__(self, graph, dim='go-terms', pos=None,
nodecolor='b', nodesize=40,
with_labels=False, name='DAG Plot')
with_labels=True, name='DAG Plot')
plots.PlotThresholder.__init__(self, "IC")
def rectangle_select_callback(self, x1, y1, x2, y2, key):
ids = self.points_in_rect(x1, y1, x2, y2, key)
ids = self.visible.intersection(ids)
ids = self.update_selection(ids, key)
self.selection_listener(self.current_dim, ids)
# def rectangle_select_callback(self, x1, y1, x2, y2, key):
# ids = self.points_in_rect(x1, y1, x2, y2, key)
# ids = self.visible.intersection(ids)
# ids = self.update_selection(ids, key)
#
# self.selection_listener(self.current_dim, ids)
def _update_color_from_dataset(self, ds):
DagPlot._update_color_from_dataset(self, ds)

2
workflows/smokers.py
View File

@ -66,6 +66,8 @@ class SmallTestWorkflow(workflow.Workflow):
# go.add_function(gobrowser.DistanceToSelectionFunction())
# go.add_function(gobrowser.TTestFunction())
go.add_function(gobrowser.PlotDagFunction())
go.add_function(gobrowser.PlotDagFunction("cc"))
go.add_function(gobrowser.PlotDagFunction("mf"))
go.add_function(GoEnrichment())
go.add_function(GoEnrichmentCond())
go.add_function(MapGO2Gene())