261 lines
8.4 KiB
Python
261 lines
8.4 KiB
Python
import gtk
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import system.workflow as wf
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from system.workflow import Stage, Function
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import pickle
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from scipy import log2,transpose,dot,divide,shape,mean,resize,zeros
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from scipy.linalg import svd,inv,norm,get_blas_funcs,eig
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from system import dataset, logger, plots
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class PCAWorkflow(wf.Workflow):
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name = 'PCA Workflow'
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ident = 'pca'
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description = 'PCA workflow. Uses real microarray data from a study of diabetes (Mootha et al.).'
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def __init__(self, app):
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wf.Workflow.__init__(self, app)
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#self.add_project(app.project)
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#logger.log('notice','Current project added to: %s' %self.name)
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load = Stage('load', 'Load Data')
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load.add_function(LoadMoothaData())
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self.add_stage(load)
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preproc = Stage('preprocess', 'Preprocessing')
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preproc.add_function(Log2Function())
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self.add_stage(preproc)
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annot = Stage('annot', 'Affy annotations')
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annot.add_function(LoadAnnotationsFunction())
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self.add_stage(annot)
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model = Stage('model', 'Model')
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model.add_function(PCAFunction(self))
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self.add_stage(model)
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logger.log('debug', '\tPCA\'s workflow is now active')
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class LoadAnnotationsFunction(Function):
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def __init__(self):
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Function.__init__(self, 'load', 'Load Annotations')
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def load_affy_file(self, filename):
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f = open(filename)
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logger.log('notice', 'Loading annotation file: %s' % filename)
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self.file = f
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def on_response(self, dialog, response):
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if response == gtk.RESPONSE_OK:
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logger.log('notice', 'Reading file: %s' % dialog.get_filename())
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self.load_affy_file(dialog.get_filename())
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def run(self,data):
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btns = ('Open', gtk.RESPONSE_OK, \
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'Cancel', gtk.RESPONSE_CANCEL)
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dialog = gtk.FileChooserDialog('Open Affy Annotation File',
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buttons=btns)
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dialog.connect('response', self.on_response)
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dialog.run()
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dialog.destroy()
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### Reading and parsing here
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annot = read_affy_annot(self.file)
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i_want = 'Pathway'
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nothing = '---'
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ids_in_data = set(data.names('genes')) #assuming we have genes
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sanity_check = set(annot.keys())
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if not ids_in_data.intersection(sanity_check) == ids_in_data:
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logger.log('debug','Some identifers in data does not exist in affy file!')
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for affy_id,description in annot:
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if affy_id in ids_in_data:
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pathways = description[i_want]
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if not pathways[0][0]=='--':
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pass
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D = []
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return [D]
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class PCAFunction(Function):
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def __init__(self,workflow):
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Function.__init__(self, 'pca', 'PCA')
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self.output = None
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self.workflow = workflow
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def run(self,data):
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logger.log('debug', 'datatype: %s' % type(data))
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if not isinstance(data,dataset.Dataset):
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return None
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#logger.log('debug', 'dimensions: %s' % data.dims)
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## calculations
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T,P,E,tsq = self.pca(data._array,5,tsq_loads=False)
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comp_def = ('comp',('1','2','3','4','5'))
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singel_def = ('1',('s'))
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# pull out input identifiers:
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row_ids = data.get_identifiers('genes')
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col_ids = data.get_identifiers('samples')
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T = dataset.Dataset(T,[('samples',col_ids) ,comp_def])
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P = dataset.Dataset(P,[('genes',row_ids),comp_def])
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E = dataset.Dataset(E,[('samples',col_ids),('genes',row_ids)])
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#tsq = dataset.Dataset(tsq,[singel_def,data_ids[1])
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## plots
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loading_plot1 = plots.ScatterPlot(P,P,'genes','comp','1','2')
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loading_plot2 = plots.ScatterPlot(P,P,'genes','comp','3','4')
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score_plot = plots.ScatterPlot(T,T,'samples','comp','1','2')
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return [T,P,E,loading_plot1,loading_plot2,score_plot]
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def pca(self,X,a_opt,cent=True,scale='loads',tsq_loads=False):
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"""Principal component analysis
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input:
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Xc -- matrix, data
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a_opt -- scalar, max number of comp. to calculate
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cent -- bool, centering [True]
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crit -- string, pc criteria ['exp_var',['ief','rpv','average']]
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scale -- string, scaling ['loads',['scores']]
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tsq_loads -- bool, calculate t-squared? [True]
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reg -- float, covariance regularizer for tsq calculations [0.2]
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output:
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T,P,E,r
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"""
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nSamples,nVarX = shape(X)
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if cent:
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Xc = self.mat_center(X)
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else:
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Xc = X
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u,s,vh = self.esvd(Xc)
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if scale=='scores':
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T = u*s
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T = T[:,:a_opt]
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P = transpose(vh)
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P = P[:,:a_opt]
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elif scale=='loads':
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T = u
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T = T[:,:a_opt]
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P = transpose(vh)*s
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P = P[:,:a_opt]
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E = Xc - dot(T,transpose(P))
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varEach = s**2
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totVar = sum(varEach)
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r = divide(varEach,totVar)*100
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return T,P,E,r
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def mat_center(self,X,axis=0,ret_mn=False):
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"""Mean center matrix along axis.
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input:
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X -- matrix, data
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axis -- dim,
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ret_mn -- bool, return mean
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output:
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Xc, [mnX]
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NB: axis = 1 is column-centering, axis=0=row-centering
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default is row centering (axis=0)
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"""
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try:
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rows,cols = shape(X)
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except ValueError:
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print "The X data needs to be two-dimensional"
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if axis==0:
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mnX = mean(X,axis)
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Xs = X - resize(mnX,(rows,cols))
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elif axis==1:
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mnX = mean(X,axis)
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Xs = transpose(transpose(X) - resize(mnX,(cols,rows)))
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if ret_mn:
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return Xs,mnX
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else:
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return Xs
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def esvd(self,data,economy=1):
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"""SVD with the option of economy sized calculation
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Calculate subspaces of X'X or XX' depending on the shape
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of the matrix.
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Good for extreme fat or thin matrices.
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"""
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mm = self.mm
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m,n = shape(data)
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if m>=n:
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u,s,v = svd(mm(data,data,trans_a=1))
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u = mm(data,v,trans_b=1)
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for i in xrange(n):
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s[i] = norm(u[:,i])
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u[:,i] = u[:,i]/s[i]
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else:
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u,s,v = svd(mm(data,data,trans_b=1))
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v = mm(u,data,trans_a=1)
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for i in xrange(m):
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s[i] = norm(v[i,:])
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v[i,:] = v[i,:]/s[i]
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return u,s,v
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def mm(self,a,b, alpha=1.0, beta=0.0, c=None, trans_a=0,
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trans_b=0):
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"""Fast matrix multiplication
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Return alpha*(a*b) + beta*c.
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a,b,c : matrices
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alpha, beta: scalars
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trans_a : 0 (a not transposed),
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1 (a transposed),
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2 (a conjugate transposed)
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trans_b : 0 (b not transposed),
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1 (b transposed),
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2 (b conjugate transposed)
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"""
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if c:
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gemm,= get_blas_funcs(('gemm',),(a,b,c))
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else:
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gemm,= get_blas_funcs(('gemm',),(a,b))
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return gemm(alpha, a, b, beta, c, trans_a, trans_b)
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class LoadMoothaData(Function):
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def __init__(self):
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Function.__init__(self, 'load', 'Load diabetes data')
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def run(self,data):
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data_file = open('full_data.pickle','r')
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data = pickle.load(data_file)
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data_file.close()
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sample_file = open('sample_labels.pickle','r')
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sample_names = pickle.load(sample_file)
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sample_file.close()
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typecode='f'
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nSamps = len(sample_names)
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nVars = len(data.keys())
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gene_ids = []
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x = zeros((nSamps,nVars),typecode)
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for i,(id,desc) in enumerate(data.items()):
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gene_ids.append(id)
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x[:,i] = desc[0].astype(typecode)
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gene_def = ('genes',gene_ids)
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sample_def = ('samples', sample_names)
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X = dataset.Dataset(x,identifiers=[sample_def,gene_def]) # samples x genes
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return [X]
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class Log2Function(Function):
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def __init__(self):
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Function.__init__(self, 'log', 'Log2')
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def run(self,data):
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x = log2(data._array)
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#pull out identifiers
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ids = []
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for dim in data.get_dim_names():
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ids.append((dim,data.get_identifiers(dim)))
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return [dataset.Dataset(x,identifiers=ids,name='Log2_X')]
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PCAWorkflow.name = 'PCA Workflow'
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