Whatnot
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@ -11,24 +11,30 @@ def plot_corrloads(R, pc1=0,pc2=1,s=20, c='b', zorder=5,expvar=None,ax=None,draw
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if ax==None or drawback==True:
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radius = 1
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center = (0,0)
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c100 = matplotlib.patches.Circle(center,radius=radius,
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facecolor='gray',
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alpha=.1,
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zorder=1)
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c50 = matplotlib.patches.Circle(center, radius=radius/2.0,
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facecolor='gray',
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alpha=.1,
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zorder=2)
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c100 = matplotlib.patches.Circle(center,
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radius=radius,
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facecolor=(0.97, .97, .97),
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zorder=1,
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linewidth=1,
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edgecolor=(0,0,0))
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c50 = matplotlib.patches.Circle(center,
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radius=radius/2.0,
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facecolor=(.85,.85,.85),
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zorder=1,
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linewidth=1,
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edgecolor=(0,0,0))
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ax = pylab.gca()
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ax.add_patch(c100)
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ax.add_patch(c50)
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ax.axhline(lw=1.5,color='k')
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ax.axvline(lw=1.5,color='k')
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ax.axhline(lw=1.5,color='k', zorder=4)
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ax.axvline(lw=1.5,color='k', zorder=4)
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# corrloads
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ax.scatter(R[:,pc1], R[:,pc2], s=s, c=c,zorder=zorder, **kwds)
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ax.set_xlim([-1,1])
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ax.set_ylim([-1,1])
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ax.set_xlim([-1.1,1.1])
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ax.set_ylim([-1.1,1.1])
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if expvar!=None:
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xstring = "Comp: %d expl.var: %.1f " %(pc1+1, expvar[pc1])
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pylab.xlabel(xstring)
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@ -51,7 +57,7 @@ def dag(terms, ontology):
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#setattr(dag, "_ontology", ontology)
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return dag
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def plot_dag(dag, node_color='b', node_size=30,with_labels=False,nodelist=None,pos=None):
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def plot_dag(dag, node_color='b', node_size=30,with_labels=False,nodelist=None,pos=None,**kwd):
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rpy.r.library("GOstats")
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@ -76,7 +82,7 @@ def plot_dag(dag, node_color='b', node_size=30,with_labels=False,nodelist=None,p
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if len(node_color)>1:
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assert(len(node_color)==len(nodelist))
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nx.draw_networkx(G,pos, with_labels=with_labels, node_size=node_size, node_color=node_color, nodelist=nodelist)
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nx.draw_networkx(G,pos, with_labels=with_labels, node_size=node_size, node_color=node_color, nodelist=nodelist, **kwd)
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return pos
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@ -4,7 +4,7 @@ import rpy
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silent_eval = rpy.with_mode(rpy.NO_CONVERSION, rpy.r)
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import collections
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def goterms_from_gene(genelist, ontology='BP', garbage=None, ic_cutoff=2.0):
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def goterms_from_gene(genelist, ontology='BP', garbage=['IEA'], ic_cutoff=2.0, verbose=False):
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""" Returns the go-terms from a specified genelist (Entrez id).
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Recalculates the information content if needed based on selected evidence codes.
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@ -30,10 +30,17 @@ def goterms_from_gene(genelist, ontology='BP', garbage=None, ic_cutoff=2.0):
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ddef = False
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if ontology=='BP' and garbage!=None:
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# This is for ont=BP and garbage =['IEA', 'ISS', 'ND']
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rpy.r.load("ICsBPIMP_IGI_IPI_ISS_IDA_IEP_TAS_NAS_IC.rda")
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rpy.r.load("ICsBP_small.rda") # Excludes IEA
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ic = rpy.r.assign("IC",rpy.r.IC, envir=rpy.r.GOSimEnv)
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print len(ic)
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max_val = 0
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for key, val in ic.items():
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if val != scipy.inf:
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if val>max_val:
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max_val = val
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for key, val in ic.items():
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ic[key] = val/max_val
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else:
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# NB! this IC is just for BP
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ic = rpy.r('get("IC", envir=GOSimEnv)')
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print "loading GO definitions environment"
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@ -42,25 +49,57 @@ def goterms_from_gene(genelist, ontology='BP', garbage=None, ic_cutoff=2.0):
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dd = 0
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ii = 0
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jj = 0
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all = rpy.r.mget(gene_ids, rpy.r.GOENTREZID2GO,ifnotfound="NA")
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kk = 0
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all = rpy.r.mget(genelist, rpy.r.GOENTREZID2GO,ifnotfound="NA")
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n_ic = len(ic)
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print "Number of terms with IC: %d" %n_ic
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stopp = False
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for gene, terms in all.items():
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if verbose:
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print "\n\n ======ITEM========\n"
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print "Gene: " + str(gene)
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print "Number of terms: %d " %len(terms)
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print terms
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print "---\n"
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if stopp:
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1/0
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if terms!="NA":
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for term,desc in terms.items():
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if desc['Ontology'].lower() == ontology and term in ic:
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if ic[term]>.88:
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for term, desc in terms.items():
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if verbose:
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print "\nChecking term: " + str(term)
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print "With description: " + str(desc)
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if desc['Ontology'].lower() == ontology.lower() and term in ic:
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if ic[term]>ic_cutoff:
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#print ic[term]
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jj+=1
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if verbose:
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print "too high" + str((gene, term))
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stopp = True
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continue
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cc+=1
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cc += 1
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if verbose:
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print "accepted" + str((gene, term))
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gene2terms[gene].append(term)
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else:
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dd+=1
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if verbose:
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print "Not accepted: " + str((gene, term))
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if term not in ic:
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if verbose:
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print "Not in IC: " + str((gene, term))
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kk+=1
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if desc['Ontology'].lower() != ontology:
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if verbose:
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print "Not in Ontology" + str((gene, term))
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dd+=1
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else:
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ii+=1
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print "\nNumber of genes without annotation: %d" %ii
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print "\nNumber of genes not in %s : %d " %(ontology, dd)
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print "\nNumber of genes with too high IC : %d " %jj
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print "Number of genes total: %d" %len(all)
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print "\nNumber of genes without annotation: (%d (NA))" %ii
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print "\nNumber of terms with annoation but no IC: %d" %kk
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print "\nNumber of terms not in %s : %d " %(ontology, dd)
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print "\nNumber of terms with too high IC : %d " %jj
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print "\n Number of accepted terms: %d" %cc
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return gene2terms
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@ -156,7 +195,7 @@ def parents_dag(go_terms, ontology=['BP']):
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def gene_GO_hypergeo_test(genelist,universe="entrezUniverse",ontology="BP",chip = "hgu133a",pval_cutoff=0.01,cond=False,test_direction="over"):
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#assert(scipy.alltrue([True for i in genelist if i in universe]))
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universeGeneIds=universe
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universeGeneIds = universe
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params = rpy.r.new("GOHyperGParams",
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geneIds=genelist,
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annotation="hgu133a",
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@ -222,5 +261,3 @@ def R_PLS(x,y,ncomp=3, validation='"LOO"'):
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result = rpy.r(callstr)
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return result
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def gogene()
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@ -1,4 +1,4 @@
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import sys
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import sys,time,cPickle
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import rpy
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from pylab import gca, figure, subplot,plot
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from scipy import *
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@ -9,70 +9,214 @@ import rpy_go
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sys.path.append("../../fluents") # home of dataset
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sys.path.append("../../fluents/lib") # home of cx_stats
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sys.path.append("/home/flatberg/fluents/scripts/lpls")
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sys.path.append("/home/flatberg/pyblm/")
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import dataset
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import cx_stats
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from engines import nipals_lpls
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from validation import lpls_val, lpls_jk
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import pyblm
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from pyblm.engines import nipals_lpls, pls
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from pyblm.crossvalidation import lpls_val, lpls_jk
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from pyblm.statistics import pls_qvals
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from plots_lpls import plot_corrloads, plot_dag
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import plots_lpls
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def iqr(X, axis=0):
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"""Interquartile range filtering."""
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def _iqr(c):
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return stats.scoreatpercentile(c, 75) - stats.scoreatpercentile(c, 25)
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return apply_along_axis(_iqr, axis, X)
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# Possible outliers
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# http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16817967
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sample_outliers = ['OV:NCI_ADR_RES', 'CNS:SF_295', 'CNS:SF_539', 'RE:SN12C', 'LC:NCI_H226', 'LC:NCI_H522', 'PR:PC_3', 'PR:DU_145']
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outlier = 'ME:LOXIMVI' # 19
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####### OPTIONS ###########
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# data
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chip = "hgu133a"
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use_data = 'uma'
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subset = 'plsr'
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small_test = False
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use_sbg_subset = True # the sandberg nci-Ygroups subset
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std_y = True
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std_z = False
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# go
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ontology = "bp"
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min_genes = 5
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similarities = ("JiangConrath","Resnik","Lin","CoutoEnriched","CoutoJiangConrath","CoutoResnik","CoutoLin")
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meth = similarities[2]
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go_term_sim = "OA"
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# lpls
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a_max = 5
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aopt = 2
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xz_alpha = .4
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w_alpha = .3
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mean_ctr = [2, 0, 2]
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nsets = None
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qval_cutoff = 0.01
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n_iter = 200
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#use_data = 'scherf'
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#use_data = 'uma'
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alpha_check = False
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calc_rmsep = False
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if use_data == 'scherf':
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data_cached = False
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use_saved_plsr_result = False
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subset = 'plsr'
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small_test = False
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use_sbg_subset = True # the sandberg nci-Ygroups subset
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std_y = False
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std_z = False
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# go
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ontology = "bp"
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min_genes = 5
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similarities = ("JiangConrath","Resnik","Lin","CoutoEnriched","CoutoJiangConrath","CoutoResnik","CoutoLin")
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meth = similarities[2]
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go_term_sim = "OA"
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# lpls
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a_max = 10
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aopt = 4
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aopt = 2 # doubling-time
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xz_alpha = .5
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w_alpha = .3
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center_axis = [2, 0, 2]
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zorth = True
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nsets = None
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qval_cutoff = 0.1
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n_iter = 50
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alpha_check = True
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calc_rmsep = True
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bevel_check = False
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save_calc = True
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elif use_data == 'uma':
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data_cached = False
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use_saved_plsr_result = False
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subset = 'iqr'
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small_test = False
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use_sbg_subset = True # the sandberg nci-Ygroups subset
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std_y = False
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std_z = False
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# go
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ontology = "bp"
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min_genes = 5
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similarities = ("JiangConrath","Resnik","Lin","CoutoEnriched","CoutoJiangConrath","CoutoResnik","CoutoLin")
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meth = similarities[2]
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go_term_sim = "OA"
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# lpls
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a_max = 10
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aopt = 5
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xz_alpha = .5
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w_alpha = .3
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center_axis = [2, 0, 2]
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zorth = True
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nsets = None
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qval_cutoff = 0.01
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n_iter = 50
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alpha_check = True
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calc_rmsep = True
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bevel_check = False
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save_calc = True
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elif use_data == 'smoker':
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data_cached = False
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use_saved_plsr_result = False
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#subset = 'plsr'
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subset = 'plsr'
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small_test = False
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use_sbg_subset = False # the sandberg nci-Ygroups subset
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std_y = False
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std_z = False
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# go
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ontology = "bp"
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min_genes = 5
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similarities = ("JiangConrath","Resnik","Lin","CoutoEnriched","CoutoJiangConrath","CoutoResnik","CoutoLin")
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meth = similarities[2]
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go_term_sim = "OA"
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# lpls
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a_max = 5
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aopt = 2
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xz_alpha = .5
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w_alpha = .3
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center_axis = [2, 0, 2]
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zorth = True
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nsets = None
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qval_cutoff = 0.01
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n_iter = 50
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alpha_check = True
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calc_rmsep = True
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bevel_check = False
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save_calc = True
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else:
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raise ValueError
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print "Using options for : " + use_data
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######## DATA ##########
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if use_data=='smoker':
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# full smoker data
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DX = dataset.read_ftsv(open("../../data/smokers-full/Smokers.ftsv"))
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DY = dataset.read_ftsv(open("../../data/smokers-full/Yg.ftsv"))
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Y = DY.asarray().astype('d')
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DX = dataset.read_ftsv(open("/home/flatberg/datasets/smokers/full/Smokers.ftsv"))
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DY = dataset.read_ftsv(open("/home/flatberg/datasets/smokers/full/Yg.ftsv"))
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DYr = dataset.read_ftsv(open("/home/flatberg/datasets/smokers/full/Ypy.ftsv"))
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Y = DYr.asarray().astype('d')
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gene_ids = DX.get_identifiers('gene_ids', sorted=True)
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sample_ids = DY.get_identifiers('_patient', sorted=True)
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elif use_data=='scherf':
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DX = dataset.read_ftsv(open("../../data/scherf/scherfX.ftsv"))
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DY = dataset.read_ftsv(open("../../data/scherf/scherfY.ftsv"))
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Yg = DY.asarray().astype('d')
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print "hepp"
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#DX = dataset.read_ftsv(open("../../data/scherf/old_data/scherfX.ftsv"))
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#DY = dataset.read_ftsv(open("../../data/scherf/old_data/scherfY.ftsv"))
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DX = dataset.read_ftsv(open("nci60/X5964.ftsv", "r"))
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DYg = dataset.read_ftsv(open("../../data/uma/Yg133.ftsv"))
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DYr = dataset.read_ftsv(open("../../data/uma/Yd.ftsv"))
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Y = DYg.asarray().astype('d')
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DY = DYg.copy()
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Yg = Y
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Yr = DYr.asarray().astype('d')
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X = DX.asarray()
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gene_ids = DX.get_identifiers('gene_ids', sorted=True)
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sample_ids = DY.get_identifiers('cline', sorted=True)
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elif use_data=='staunton':
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pass
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elif use_data=='uma':
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DX = dataset.read_ftsv(open("../../data/uma/X133.ftsv"))
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DYg = dataset.read_ftsv(open("../../data/uma/Yg133.ftsv"))
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DY = dataset.read_ftsv(open("../../data/uma/Yd.ftsv"))
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Y = DY.asarray().astype('d')
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Yg = DYg.asarray().astype('d')
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gene_ids = DX.get_identifiers('gene_ids', sorted=True)
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# use subset with defined GO-terms
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elif use_data=='uma':
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DX = dataset.read_ftsv(open("/home/flatberg/datasets/uma/X133.ftsv"))
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DYg = dataset.read_ftsv(open("/home/flatberg/datasets/uma/Yg133.ftsv"))
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DYr = dataset.read_ftsv(open("/home/flatberg/datasets/uma/Yd.ftsv"))
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X = DX.asarray()
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Y = DYg.asarray().astype('d')
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DY = DYg.copy()
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Yg = Y
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Yr = DYr.asarray().astype('d')
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gene_ids = DX.get_identifiers('gene_ids', sorted=True)
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sample_ids = DY.get_identifiers('cline', sorted=True)
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else:
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print "use_data argument: (%s) not valid" %use_method
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if use_sbg_subset and use_data in ['uma', 'scherf', 'staunton']:
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print "Using sbg subset of cancers"
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Y = Yg
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Y_old = Y.copy()
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Yr_old = Yr.copy()
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X_old = X.copy()
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keep_samples = ['CN', 'ME', 'LE', 'CO', 'RE']
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#keep_samples = ['CN', 'ME', 'LE', 'CO', 'RE']
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sample_ids_original = DY.get_identifiers('cline', sorted=True)
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sample_ids= [i for i in sample_ids if i[:2] in keep_samples]
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rows_ind = [i for i,name in enumerate(sample_ids_original) if name[:2] in keep_samples]
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# take out rows in X,Y
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X = X[rows_ind,:]
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Y = Y[rows_ind,:]
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Yr = Yr[rows_ind,:]
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# identify redundant columns in Y
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cols_ind = where(Y.sum(0)>1)[0]
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Y = Y[:, cols_ind]
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# create new datasets with updated idents
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cat_ids = [name for i,name in enumerate(DYg.get_identifiers('_cancer', sorted=True)) if i in cols_ind]
|
||||
DX = dataset.Dataset(X, [['cline', sample_ids], ['gene_ids', gene_ids]], name='Dxr')
|
||||
DYg = dataset.CategoryDataset(Y, [['cline', sample_ids], ['_cancer', cat_ids]], name='Dyr')
|
||||
DYr = dataset.Dataset(Yr, [['cline', sample_ids], ['_time', ['doubling_time']]], name='Dyrr')
|
||||
DY_old = DY.copy()
|
||||
DY = DYg
|
||||
print "Now there are %d samples in X" %X.shape[0]
|
||||
|
||||
# use subset of genes with defined GO-terms
|
||||
ic_all = 2026006.0 # sum of all ic in BP
|
||||
max_ic = -log(1/ic_all)
|
||||
ic_cutoff = -log(min_genes/ic_all)/max_ic
|
||||
|
|
@ -99,30 +243,63 @@ print "\n\nFiltering genes by Go terms "
|
|||
|
||||
# use subset based on SAM,PLSR or (IQR)
|
||||
|
||||
if subset=='sam':
|
||||
# select subset genes by SAM
|
||||
rpy.r.library("siggenes")
|
||||
rpy.r.library("qvalue")
|
||||
rpy.r.assign("data", X.T)
|
||||
cl = dot(DYg.asarray(), diag(arange(Yg.shape[1])+1)).sum(1)
|
||||
rpy.r.assign("cl", cl)
|
||||
rpy.r.assign("B", 20)
|
||||
# Perform a SAM analysis.
|
||||
print "Starting SAM"
|
||||
sam = rpy.r('sam.out<-sam(data=data,cl=cl,B=B,rand=123)')
|
||||
print "SAM done"
|
||||
# Compute the q-values of the genes.
|
||||
qq = rpy.r('qobj<-qvalue(sam.out@p.value)')
|
||||
qvals = asarray(qq['qvalues'])
|
||||
# cut off
|
||||
cutoff = 0.001
|
||||
index = where(qvals<cutoff)[0]
|
||||
if small_test:
|
||||
index = index[:20]
|
||||
if subset=='plsr':
|
||||
print "plsr filter on genes"
|
||||
if use_saved_plsr_result:
|
||||
index = cPickle.load(open('plsr_index.pkl'))
|
||||
# Subset data
|
||||
X = X[:,index]
|
||||
|
||||
# Subset data
|
||||
gene_ids = [gid for i, gid in enumerate(gene_ids) if i in index]
|
||||
print "\nNumber of genes: %s" %len(gene_ids)
|
||||
print "\nWorking on subset with %s genes " %len(gene_ids)
|
||||
|
||||
# update valid go-terms
|
||||
gene2goterms = rpy_go.goterms_from_gene(gene_ids, ic_cutoff=ic_cutoff)
|
||||
all_terms = set()
|
||||
for t in gene2goterms.values():
|
||||
all_terms.update(t)
|
||||
terms = list(all_terms)
|
||||
print "\nNumber of go-terms: %s" %len(terms)
|
||||
# update genelist
|
||||
gene_ids = gene2goterms.keys()
|
||||
else:
|
||||
|
||||
print "Initial plsr qvals"
|
||||
|
||||
xcal_tsq_x, xpert_tsq_x = pyblm.pls_qvals(X, Y, aopt=aopt, n_iter=n_iter, center_axis=[0,0], nsets=None)
|
||||
qvals = pyblm.statistics._fdr(xcal_tsq_x, xpert_tsq_x, median)
|
||||
|
||||
# cut off
|
||||
#sort_index = qvals.argsort()
|
||||
#index = sort_index[:800]
|
||||
#qval_cutoff = qvals[sort_index[500]]
|
||||
print "Using cuf off: %.2f" %qval_cutoff
|
||||
index = where(qvals<qval_cutoff)[0]
|
||||
if small_test:
|
||||
index = index[:20]
|
||||
# Subset data
|
||||
X = X[:,index]
|
||||
|
||||
gene_ids = [gid for i, gid in enumerate(gene_ids) if i in index]
|
||||
print "\nNumber of genes: %s" %len(gene_ids)
|
||||
print "\nWorking on subset with %s genes " %len(gene_ids)
|
||||
|
||||
# update valid go-terms
|
||||
gene2goterms = rpy_go.goterms_from_gene(gene_ids, ic_cutoff=ic_cutoff)
|
||||
all_terms = set()
|
||||
for t in gene2goterms.values():
|
||||
all_terms.update(t)
|
||||
terms = list(all_terms)
|
||||
print "\nNumber of go-terms: %s" %len(terms)
|
||||
# update genelist
|
||||
gene_ids = gene2goterms.keys()
|
||||
print "\nNumber of genes: %s" %len(gene_ids)
|
||||
|
||||
elif subset == 'iqr':
|
||||
iqr_vals = iqr(X)
|
||||
index = where(iqr_vals>1)[0]
|
||||
X = X[:,index]
|
||||
|
||||
gene_ids = [gid for i, gid in enumerate(gene_ids) if i in index]
|
||||
print "\nNumber of genes: %s" %len(gene_ids)
|
||||
print "\nWorking on subset with %s genes " %len(gene_ids)
|
||||
|
|
@ -136,11 +313,9 @@ if subset=='sam':
|
|||
print "\nNumber of go-terms: %s" %len(terms)
|
||||
# update genelist
|
||||
gene_ids = gene2goterms.keys()
|
||||
print "\nNumber of genes: %s" %len(gene_ids)
|
||||
elif subset=='plsr':
|
||||
cx_stats.pls_qvals(X, Y)
|
||||
else:
|
||||
# noimp (smoker data is prefiltered)
|
||||
print "No prefiltering on data used"
|
||||
pass
|
||||
|
||||
|
||||
|
|
@ -154,40 +329,91 @@ if meth=="CoutoEnriched":
|
|||
aa = 0
|
||||
ba = 0
|
||||
rpy.r.setEnrichmentFactors(alpha = aa, beta =ba)
|
||||
rpytmat = rpy.with_mode(rpy.NO_CONVERSION, rpy.r.getTermSim)(terms, method=meth,verbose=False)
|
||||
tmat = rpy.r.assign("haha", rpytmat)
|
||||
print "\n Calculating Z matrix"
|
||||
Z = rpy_go.genego_sim(gene2goterms,gene_ids,terms,rpytmat,go_term_sim=go_term_sim,term_sim=meth)
|
||||
|
||||
# update data (X) matrix
|
||||
newind = DX.get_indices('gene_ids', gene_ids)
|
||||
Xr = DX.asarray()[:,newind]
|
||||
|
||||
|
||||
######## LPLSR ########
|
||||
print "LPLSR ..."
|
||||
Y = Yg
|
||||
|
||||
if use_sbg_subset:
|
||||
Y_old = Y.copy()
|
||||
Xr_old = Xr.copy()
|
||||
keep_samples = ['CN', 'ME', 'LE', 'CO', 'RE']
|
||||
sample_ids = DY.get_identifiers('cline', sorted=True)
|
||||
keep_ind = [i for i,name in enumerate(sample_ids) if name[:2] in keep_samples]
|
||||
Xr = Xr[keep_ind,:]
|
||||
Y = Y[keep_ind,:]
|
||||
Y = Y[:, where(Y.sum(0)>1)[0]]
|
||||
if not data_cached:
|
||||
rpytmat = rpy.with_mode(rpy.NO_CONVERSION, rpy.r.getTermSim)(terms, method=meth,verbose=False)
|
||||
tmat = rpy.r.assign("haha", rpytmat)
|
||||
print "\n Calculating Z matrix"
|
||||
Z = rpy_go.genego_sim(gene2goterms,gene_ids,terms,rpytmat,go_term_sim=go_term_sim,term_sim=meth)
|
||||
|
||||
DZ = dataset.Dataset(Z, [['go-terms', terms], ['gene_ids', gene_ids]], name='Dz_'+str(meth))
|
||||
# update data (X) matrix
|
||||
newind = DX.get_indices('gene_ids', gene_ids)
|
||||
Xr = DX.asarray()[:,newind]
|
||||
DXr = dataset.Dataset(Xr, [['cline', sample_ids], ['gene_ids', gene_ids]], name='Dxr')
|
||||
else:
|
||||
#DXr = dataset.read_ftsv(open('Xr.ftsv', 'r'))
|
||||
newind = DX.get_indices('gene_ids', gene_ids)
|
||||
Xr = DX.asarray()[:,newind]
|
||||
DXr = dataset.Dataset(Xr, [['cline', sample_ids], ['gene_ids', gene_ids]], name='Dxr')
|
||||
DY = dataset.read_ftsv(open('Y.ftsv', 'r'))
|
||||
DZ = dataset.read_ftsv(open('Z.ftsv', 'r'))
|
||||
Xr = DXr.asarray()
|
||||
Y = DY.asarray()
|
||||
Z = DZ.asarray()
|
||||
sample_ids = DX.get_identifiers('cline', sorted=True)
|
||||
|
||||
# standardize Z?
|
||||
sdtz = False
|
||||
if sdtz:
|
||||
Z = Z/Z.std(0)
|
||||
|
||||
sdty = True
|
||||
DZ._array = DZ._array/Dz._array.std(0)
|
||||
sdty = False
|
||||
if sdty:
|
||||
Y = Y/Y.std(0)
|
||||
lpls_result = nipals_lpls(Xr,Y,Z, a_max,alpha=xz_alpha,mean_ctr=mean_ctr)
|
||||
DY._array = DY._array/DY._array.std(0)
|
||||
|
||||
|
||||
# ##### PLS ONLY, CHECK FOR SIMILARITY BETWEEN W and Z #######
|
||||
if bevel_check:
|
||||
Xr = DXr.asarray()
|
||||
Y = DY.asarray()
|
||||
from pylab import figure, scatter, xlabel, subplot,xticks,yticks
|
||||
Xrcc = Xr - Xr.mean(0) - Xr.mean(1)[:,newaxis] + Xr.mean()
|
||||
Zcc = Z - Z.mean(0) - Z.mean(1)[:,newaxis] + Z.mean()
|
||||
Yc = Y - Y.mean(0)
|
||||
xy_pls_result = pls(Xrcc, Yc, a_max)
|
||||
xz_pls_result = pls(Xrcc.T, Zcc.T, a_max)
|
||||
# check for linearity between scores of xz-result and W of xy-result
|
||||
Wxy = xy_pls_result['W']
|
||||
Txz = xz_pls_result['T']
|
||||
figure()
|
||||
n = 0
|
||||
for i in range(a_max):
|
||||
w = Wxy[:,i]
|
||||
for j in range(a_max):
|
||||
n += 1
|
||||
t = Txz[:,j]
|
||||
r2 = stats.corrcoef(w, t)[0,-1]
|
||||
subplot(a_max, a_max, n)
|
||||
scatter(w, t)
|
||||
xticks([])
|
||||
yticks([])
|
||||
xlabel('(Wxy(%d), Tzx(%d)), r2: %.1f ' %(i+1,j+1,r2))
|
||||
# ####### LPLSR ########
|
||||
|
||||
if save_calc and not data_cached:
|
||||
print "Saving calculations"
|
||||
import cPickle
|
||||
fh = open("g2go_s.pkl", "w")
|
||||
cPickle.dump(gene2goterms, fh)
|
||||
fh.close()
|
||||
dataset.write_ftsv(open('Xs.ftsv', 'w'), DXr, decimals=7)
|
||||
dataset.write_ftsv(open('Ysg.ftsv', 'w'), DY, decimals=7)
|
||||
dataset.write_ftsv(open('Yspy.ftsv', 'w'), DYr, decimals=7)
|
||||
dataset.write_ftsv(open('Zs.ftsv', 'w'), DZ, decimals=7)
|
||||
|
||||
def read_calc():
|
||||
import cPickle
|
||||
fh = open("g2go_s.pkl")
|
||||
gene2goterms = cPickle.load(fh)
|
||||
fh.close()
|
||||
DXr = dataset.read_ftsv('Xu.ftsv')
|
||||
DY = dataset.read_ftsv('Yu.ftsv')
|
||||
DYr = dataset.read_ftsv('Ydu.ftsv')
|
||||
DZ = dataset.read_ftsv('Zu.ftsv')
|
||||
return DXr, DY, DYr, DZ, gene2goterms
|
||||
|
||||
|
||||
print "LPLSR ..."
|
||||
lpls_result = nipals_lpls(Xr,Y,Z, a_max,alpha=xz_alpha, center_axis=center_axis, zorth=zorth)
|
||||
globals().update(lpls_result)
|
||||
|
||||
# Correlation loadings
|
||||
|
|
@ -197,46 +423,75 @@ cadz,Rz,rssz = correlation_loadings(Z.T, W, L)
|
|||
|
||||
# Prediction error
|
||||
if calc_rmsep:
|
||||
rmsep , yhat, class_error = lpls_val(Xr, Y, Z, a_max, alpha=xz_alpha,mean_ctr=mean_ctr)
|
||||
|
||||
rmsep , yhat, class_error = pyblm.crossvalidation.lpls_val(Xr, Y, Z, a_max, alpha=xz_alpha,center_axis=center_axis, nsets=nsets,zorth=zorth)
|
||||
|
||||
Alpha = arange(0.0, 1.01, .05)
|
||||
if alpha_check:
|
||||
Alpha = arange(0.01, 1, .1)
|
||||
Rmsep,Yhat, CE = [],[],[]
|
||||
for a in Alpha:
|
||||
print "alpha %f" %a
|
||||
rmsep , yhat, ce = lpls_val(Xr, Y, Z, a_max, alpha=a,mean_ctr=mean_ctr,nsets=nsets)
|
||||
Rmsep.append(rmsep.copy())
|
||||
#Yhat.append(yhat.copy())
|
||||
#CE.append(ce.copy())
|
||||
rmsep_a , yhat, ce = pyblm.lpls_val(Xr, Y, Z, a_max, alpha=a,
|
||||
center_axis=center_axis,nsets=nsets,
|
||||
zorth=zorth)
|
||||
Rmsep.append(rmsep_a.copy())
|
||||
Yhat.append(yhat.copy())
|
||||
CE.append(ce.copy())
|
||||
Rmsep = asarray(Rmsep)
|
||||
#Yhat = asarray(Yhat)
|
||||
Yhat = asarray(Yhat)
|
||||
#CE = asarray(CE)
|
||||
|
||||
random_alpha_check = True
|
||||
if random_alpha_check:
|
||||
n_zrand = 100
|
||||
RMS,YHAT, CEE = [],[],[]
|
||||
zindex = arange(Z.shape[1])
|
||||
for ii in range(n_zrand):
|
||||
zind_rand = zindex.copy()
|
||||
random.shuffle(zind_rand)
|
||||
Zrand = Z[:,zind_rand]
|
||||
#Alpha = arange(0.0, 1.1, .25)
|
||||
Rmsep_r,Yhat_r, CE_r = [],[],[]
|
||||
for a in Alpha:
|
||||
print "Iter: %d alpha %.2f" %(ii, a)
|
||||
rmsep , yhat, ce = pyblm.lpls_val(Xr, Y, Zrand, a_max, alpha=a,center_axis=center_axis,nsets=nsets, zorth=zorth)
|
||||
Rmsep_r.append(rmsep.copy())
|
||||
Yhat_r.append(yhat.copy())
|
||||
CE_r.append(ce.copy())
|
||||
RMS.append(Rmsep_r)
|
||||
YHAT.append(Yhat_r)
|
||||
CEE.append(CE_r)
|
||||
RMS = asarray(RMS)
|
||||
YHAT = asarray(YHAT)
|
||||
CEE = asarray(CEE)
|
||||
|
||||
# Significance Hotellings T
|
||||
#Wx, Wz = lpls_jk(Xr, Y, Z, aopt, mean_ctr=mean_ctr, xz_alpha=xz_alpha, nsets=nsets)
|
||||
#Ws = W*apply_along_axis(norm, 0, T)
|
||||
#tsqx = cx_stats.hotelling(Wx, Ws[:,:aopt], alpha=w_alpha)
|
||||
#tsqz = cx_stats.hotelling(Wz, L[:,:aopt], alpha=0)
|
||||
calc_qvals = True
|
||||
if not calc_qvals:
|
||||
Wx, Wz = pyblm.crossvalidation.lpls_jk(Xr, Y, Z, aopt, center_axis=center_axis, xz_alpha=xz_alpha, nsets=nsets)
|
||||
Ws = W*apply_along_axis(norm, 0, T)
|
||||
Ws = Ws[:,:aopt]
|
||||
cal_tsq_x = pyblm.statistics.hotelling(Wx, Ws[:,:aopt], alpha=w_alpha)
|
||||
Ls = L*apply_along_axis(norm, 0, K)
|
||||
cal_tsq_z = pyblm.statistics.hotelling(Wz, Ls[:,:aopt], alpha=0.01)
|
||||
|
||||
# qvals
|
||||
cal_tsq_z, pert_tsq_z, cal_tsq_x, pert_tsq_x = cx_stats.lpls_qvals(Xr, Y, Z, aopt=aopt, zx_alpha=xz_alpha, n_iter=n_iter)
|
||||
|
||||
qvalz = cx_stats.fdr(cal_tsq_z, pert_tsq_z, 'median')
|
||||
qvalx = cx_stats.fdr(cal_tsq_x, pert_tsq_x, 'median')
|
||||
if calc_qvals:
|
||||
cal_tsq_z, pert_tsq_z, cal_tsq_x, pert_tsq_x = pyblm.lpls_qvals(Xr, Y, Z, aopt=aopt, zx_alpha=xz_alpha, n_iter=n_iter, nsets=nsets)
|
||||
|
||||
qvalz = pyblm.statistics._fdr(cal_tsq_z, pert_tsq_z, median)
|
||||
qvalx = pyblm.statistics._fdr(cal_tsq_x, pert_tsq_x, median)
|
||||
|
||||
|
||||
# p-values, set-enrichment analysis
|
||||
active_genes_ids = where(qvalx < qval_cutoff)[0]
|
||||
active_genes = [name for i,name in enumerate(gene_ids) if i in active_genes_ids]
|
||||
active_universe = gene_ids
|
||||
gsea_result, gsea_params= rpy_go.gene_GO_hypergeo_test(genelist=active_genes,universe=active_universe,chip=chip,pval_cutoff=1.0,cond=False,test_direction="over")
|
||||
active_goterms_ids = where(qvalz < qval_cutoff)[0]
|
||||
active_goterms = [name for i,name in enumerate(terms) if i in active_goterms_ids]
|
||||
|
||||
gsea_t2p = dict(zip(gsea_result['GOBPID'], gsea_result['Pvalue']))
|
||||
# p-values, set-enrichment analysis
|
||||
active_genes_ids = where(qvalx < qval_cutoff)[0]
|
||||
active_genes = [name for i,name in enumerate(gene_ids) if i in active_genes_ids]
|
||||
active_universe = gene_ids
|
||||
gsea_result, gsea_params= rpy_go.gene_GO_hypergeo_test(genelist=active_genes,universe=active_universe,chip=chip,pval_cutoff=1.0,cond=False,test_direction="over")
|
||||
active_goterms_ids = where(qvalz < qval_cutoff)[0]
|
||||
active_goterms = [name for i,name in enumerate(terms) if i in active_goterms_ids]
|
||||
|
||||
gsea_t2p = dict(zip(gsea_result['GOBPID'], gsea_result['Pvalue']))
|
||||
|
||||
|
||||
|
||||
|
|
@ -247,22 +502,35 @@ from scipy import where
|
|||
dg = plots_lpls.dag(terms, "bp")
|
||||
pos = None
|
||||
|
||||
figure(300)
|
||||
subplot(2,1,1)
|
||||
pos = plots_lpls.plot_dag(dg, node_color=cal_tsq_z, pos=pos, nodelist=terms)
|
||||
subplot(2,1,2)
|
||||
pos = plot_dag(dg, node_color=qvalz, pos=pos, nodelist=terms)
|
||||
|
||||
if calc_qvals:
|
||||
figure(300)
|
||||
subplot(2,1,1)
|
||||
pos = plots_lpls.plot_dag(dg, node_color=cal_tsq_z, pos=pos, nodelist=terms)
|
||||
ax = gca()
|
||||
colorbar(ax.collections[0])
|
||||
xlabel('q values')
|
||||
xticks([])
|
||||
yticks([])
|
||||
subplot(2,1,2)
|
||||
pos = plot_dag(dg, node_color=qvalz, pos=pos, nodelist=terms)
|
||||
ax = gca()
|
||||
colorbar(ax.collections[0])
|
||||
xlabel('T2 values')
|
||||
else:
|
||||
figure(300)
|
||||
subplot(2,1,1)
|
||||
pos = plots_lpls.plot_dag(dg, pos=pos, nodelist=terms)
|
||||
|
||||
if calc_rmsep:
|
||||
figure(1) #rmsep
|
||||
bar_w = .2
|
||||
bar_col = 'rgb'*5
|
||||
figure(190) #rmsep
|
||||
|
||||
bar_col = 'rgbcmyk'*2
|
||||
m = Y.shape[1]
|
||||
bar_w = 1./(m + 2.)
|
||||
for a in range(m):
|
||||
bar(arange(a_max)+a*bar_w+.1, rmsep[:,a], width=bar_w, color=bar_col[a])
|
||||
bar(arange(a_max)+a*bar_w+.1, rmsep[a,:], width=bar_w, color=bar_col[a])
|
||||
ylim([rmsep.min()-.05, rmsep.max()+.05])
|
||||
title('RMSEP: Y(%s)' %Y.get_name())
|
||||
title('RMSEP: Y(%s)' %DY.get_name())
|
||||
|
||||
#figure(2)
|
||||
#for a in range(m):
|
||||
|
|
@ -270,26 +538,28 @@ if calc_rmsep:
|
|||
#ylim([class_error.min()-.05, class_error.max()+.05])
|
||||
#title('Classification accuracy')
|
||||
|
||||
figure(3) # Hyploid correlations
|
||||
figure(5) # Hyploid correlations
|
||||
pc1 = 2
|
||||
pc2 = 3
|
||||
tsqz = cal_tsq_z
|
||||
tsqx = cal_tsq_x
|
||||
tsqz_s = 250*tsqz/tsqz.max()
|
||||
tsqz_s = 550*tsqz/tsqz.max()
|
||||
td = rpy_go.goterm2desc(terms)
|
||||
tlabels = [td[i] for i in terms]
|
||||
keep = where(qvalz<0.01)[0]
|
||||
k_Rz = Rz[keep,:]
|
||||
k_tsqz_s = tsqz_s[keep]
|
||||
k_tsq = tsqz[keep]
|
||||
k_tlabels = [name for i,name in enumerate(tlabels) if i in keep]
|
||||
plot_corrloads(Rz, pc1=0, pc2=1, s=tsqz_s, c=tsqz, zorder=5, expvar=evz, ax=None,alpha=.5,labels=None)
|
||||
#keep = tsqz.argsort()[:100]
|
||||
#k_Rz = Rz[keep,:]
|
||||
#k_tsqz_s = tsqz_s[keep]
|
||||
#k_tsq = tsqz[keep]
|
||||
#k_tlabels = [name for i,name in enumerate(tlabels) if i in keep]
|
||||
plot_corrloads(Rz, pc1=pc1, pc2=pc2, s=tsqz_s, c=tsqz, zorder=6, expvar=evz, ax=None,alpha=.9,labels=None)
|
||||
#plot_corrloads(k_Rz, pc1=0, pc2=1, s=k_tsqz_s, c=k_tsqz, zorder=5, expvar=evz, ax=None,alpha=.5,labels=None)
|
||||
ax = gca()
|
||||
yglabels = DYg.get_identifiers(DYg.get_dim_name()[1], sorted=True)
|
||||
ylabels = DY.get_identifiers(DY.get_dim_name()[1], sorted=True)
|
||||
blabels = yglabels[:]
|
||||
blabels.append(ylabels[0])
|
||||
plot_corrloads(Ry, pc1=0, pc2=1, s=150, c='g', marker='s', zorder=5, expvar=evy, ax=ax,labels=None,alpha=.9)
|
||||
plot_corrloads(Rx, pc1=0, pc2=1, s=5, c='k', zorder=1, expvar=evx, ax=ax)
|
||||
ylabels = DYg.get_identifiers(DYg.get_dim_name()[1], sorted=True)
|
||||
#ylabels = DYr.get_identifiers(DYr.get_dim_name()[1], sorted=True)
|
||||
#blabels = yglabels[:]
|
||||
#blabels.append(ylabels[0])
|
||||
plot_corrloads(Ry, pc1=pc1, pc2=pc2, s=350, c='g', marker='s', zorder=7, expvar=evy, ax=ax,labels=ylabels,alpha=1.0, drawback=False)
|
||||
plot_corrloads(Rx, pc1=pc1, pc2=pc2, s=3, c=(.6,.6,.6), alpha=1, zorder=4, expvar=evx, ax=ax, drawback=False, faceted=False)
|
||||
|
||||
|
||||
figure(4)
|
||||
|
|
@ -299,7 +569,7 @@ plot_corrloads(Rx, pc1=0, pc2=1, s=tsqx/2.0, c='b', zorder=5, expvar=evx, ax=ax)
|
|||
# title('X correlation')
|
||||
subplot(222)
|
||||
ax = gca()
|
||||
plot_corrloads(Ry, pc1=0, pc2=1, s=150, c='g', zorder=5, expvar=evy, ax=ax)
|
||||
plot_corrloads(Ry, pc1=0, pc2=1, s=250, c='g', zorder=5, expvar=evy, ax=ax)
|
||||
#title('Y correlation')
|
||||
subplot(223)
|
||||
ax = gca()
|
||||
|
|
@ -312,4 +582,73 @@ plot(evz, 'r', label='Z', linewidth=2)
|
|||
legend(loc=2)
|
||||
ylabel('Explained variance')
|
||||
xlabel('Component')
|
||||
xticks((arange(len(evx))), [str(int(i+1)) for i in arange(len(evx))])
|
||||
show()
|
||||
|
||||
|
||||
figure(19)
|
||||
#subplot(1,2,1)
|
||||
# RMS : (n_rand_iter, n_alpha, nvarY, a_max)
|
||||
# Rmsep : (n_alpha, nvarY, a_max)
|
||||
|
||||
rms = RMS[:,:,:,aopt] # looking at solution at aopt
|
||||
m_rms = rms.mean(2) # mean over all y-variables
|
||||
mm_rms = m_rms.mean(0) # mean over iterations
|
||||
std_mrms = m_rms.std(0) # standard deviation over iterations
|
||||
|
||||
rms_t = Rmsep[:,:,aopt]
|
||||
m_rms_t = rms_t.mean(1)
|
||||
xax = arange(mm_rms.shape[0])
|
||||
std2_lim_down = mm_rms - 1.*std_mrms
|
||||
std2_lim_up = mm_rms + 1.*std_mrms
|
||||
xx = r_[xax, xax[::-1]]
|
||||
yy = r_[std2_lim_down, std2_lim_up[::-1]]
|
||||
fill(xx, yy, fc='.9')
|
||||
plot(mm_rms, '--r', lw=1.5, label='Perm. mean')
|
||||
plot(std2_lim_down, 'b--')
|
||||
plot(std2_lim_up, 'b--', label='Perm. 2*std')
|
||||
plot(m_rms_t, 'g', lw=1.5, label='True')
|
||||
#c_ylim = ylim()
|
||||
#ylim(c_ylim[0], c_ylim[1]-1)
|
||||
alpha_ind = linspace(0, Alpha.shape[0]-1, 11)
|
||||
xticks(alpha_ind, ['%.1f' %a for a in arange(0,1.01, .1)])
|
||||
xlabel(r'$\alpha$')
|
||||
ylabel('mean error')
|
||||
leg = legend(loc=2)
|
||||
# delete fill from legend
|
||||
del leg.texts[-1]
|
||||
del leg.legendHandles[-1]
|
||||
# delete one of the std legends
|
||||
del leg.texts[1]
|
||||
del leg.legendHandles[1]
|
||||
|
||||
klass = True
|
||||
|
||||
if klass:
|
||||
figure(20)
|
||||
# subplot(1,2,1)
|
||||
# RMS : (n_rand_iter, n_alpha, nvarY, a_max)
|
||||
# Rmsep : (n_alpha, nvarY, a_max)
|
||||
|
||||
cee = CEE[:,:,aopt,:] # looking at solution at aopt
|
||||
m_cee = cee.mean(-1) # mean over all y-variables
|
||||
mm_cee = m_cee.mean(0) # mean over iterations
|
||||
std_cee = m_cee.std(0) # standard deviation over iterations
|
||||
CE = asarray(CE)
|
||||
cee_t = CE[:,:,aopt]
|
||||
m_cee_t = cee_t.mean(1)
|
||||
xax = arange(mm_cee.shape[0])
|
||||
std2_lim_down = mm_cee - 2*std_cee
|
||||
std2_lim_up = mm_cee + 2*std_cee
|
||||
xx = r_[xax, xax[::-1]]
|
||||
yy = r_[std2_lim_down, std2_lim_up[::-1]]
|
||||
fill(xx, yy, fc='.9')
|
||||
plot(mm_cee, '--r', lw=1.5)
|
||||
plot(std2_lim_down, 'b--')
|
||||
plot(std2_lim_up, 'b--')
|
||||
plot(m_cee_t, 'g', lw=1.5)
|
||||
c_ylim = ylim()
|
||||
ylim = ylim(c_ylim[0], .2)
|
||||
xticks(xax, [str(a)[:3] for a in Alpha])
|
||||
xlabel(r'$\alpha$')
|
||||
ylabel('mean error')
|
||||
|
|
|
|||
Reference in New Issue