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This commit is contained in:
Arnar Flatberg
2006-08-28 12:06:05 +00:00
parent 7eb3fa8b46
commit 97e652edce
7 changed files with 91 additions and 50 deletions
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8
workflows/pca_workflow.py
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@@ -6,6 +6,8 @@ from scipy import log2,transpose,dot,divide,shape,mean,resize,zeros
from scipy.linalg import svd,inv,norm,get_blas_funcs,eig
from system import dataset, logger, plots
class PCAWorkflow(wf.Workflow):
name = 'PCA Workflow'
ident = 'pca'
@@ -96,9 +98,9 @@ class PCAFunction(Function):
row_ids = data.get_identifiers('genes')
col_ids = data.get_identifiers('samples')
T = dataset.Dataset(T,[('samples',col_ids) ,comp_def])
P = dataset.Dataset(P,[('genes',row_ids),comp_def])
E = dataset.Dataset(E,[('samples',col_ids),('genes',row_ids)])
T = dataset.Dataset(T,[('samples',col_ids) ,comp_def],name='T2')
P = dataset.Dataset(P,[('genes',row_ids),comp_def],name='P')
E = dataset.Dataset(E,[('samples',col_ids),('genes',row_ids)],name='E')
#tsq = dataset.Dataset(tsq,[singel_def,data_ids[1])
## plots