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Changed use of Dataset.get_matrix() to Dataset.asarray() and removed it.

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Truls Alexander Tangstad 2006-05-05 14:43:53 +00:00
parent 97f56f66ac
commit 0db25f1dd7
4 changed files with 4 additions and 8 deletions
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4
system/dataset.py
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@ -160,10 +160,6 @@ class Dataset:
"""Returns dataset name""" """Returns dataset name"""
return self._name return self._name
def get_matrix(self):
"""Returns internal numeric matrix for dataset."""
return self._array
def get_all_dims(self): def get_all_dims(self):
"""Returns all dimensions in project""" """Returns all dimensions in project"""
return self._all_dims return self._all_dims

4
system/plots.py
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@ -386,7 +386,7 @@ class LinePlot(Plot):
import rpy import rpy
silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r) silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", dataset.get_matrix()) rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", dataset.asarray())
ymin, ymax = rpy.r("range(m)*1.1") ymin, ymax = rpy.r("range(m)*1.1")
self._ymin, self._ymax = ymin, ymax self._ymin, self._ymax = ymin, ymax
silent_eval("res <- apply(m, 2, density, from=%s, to=%s)" % (ymin, ymax)) silent_eval("res <- apply(m, 2, density, from=%s, to=%s)" % (ymin, ymax))
@ -420,7 +420,7 @@ class LinePlot(Plot):
ids = selection[dim_2] # current identifiers ids = selection[dim_2] # current identifiers
index = [ind for id,ind in self._dataset[dim_2].items() if id in ids] #conversion to index index = [ind for id,ind in self._dataset[dim_2].items() if id in ids] #conversion to index
for i in index: for i in index:
line = self._dataset.get_matrix()[i] line = self._dataset.asarray()[i]
self.ax.plot(range(1, len(line)+1), line) self.ax.plot(range(1, len(line)+1), line)
self.ax.set_xlim((0.5, cols+0.5)) self.ax.set_xlim((0.5, cols+0.5))

2
workflows/affy_workflow.py
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@ -203,7 +203,7 @@ class PCAFunction(workflow.Function):
dim_2, dim_1 = data.get_dim_names() dim_2, dim_1 = data.get_dim_names()
silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r) silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", data.get_matrix()) rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", data.asarray())
silent_eval("t = prcomp(t(m))") silent_eval("t = prcomp(t(m))")
# we make a unique name for component dimension # we make a unique name for component dimension

2
workflows/go_workflow.py
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@ -236,7 +236,7 @@ class PCAFunction(workflow.Function):
silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r) silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", data.get_matrix()) rpy.with_mode(rpy.NO_CONVERSION, rpy.r.assign)("m", data.asarray())
silent_eval("t = prcomp(t(m))") silent_eval("t = prcomp(t(m))")
T_ids = map(str, range(1, rpy.r("dim(t$x)")[1]+1)) T_ids = map(str, range(1, rpy.r("dim(t$x)")[1]+1))