randomjohn/project

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 from PIL import Image,ImageDraw def readfile(filename): lines=[line for line in file(filename)] # First line is the column titles colnames=lines[0].strip().split('\t')[1:] rownames=[] data=[] for line in lines[1:]: p=line.strip().split('\t') # First column in each row is the rowname rownames.append(p[0]) # The data for this row is the remainder of the row data.append([float(x) for x in p[1:]]) return rownames,colnames,data from math import sqrt def pearson(v1,v2): # Simple sums sum1=sum(v1) sum2=sum(v2) # Sums of the squares sum1Sq=sum([pow(v,2) for v in v1]) sum2Sq=sum([pow(v,2) for v in v2]) # Sum of the products pSum=sum([v1[i]*v2[i] for i in range(len(v1))]) # Calculate r (Pearson score) num=pSum-(sum1*sum2/len(v1)) den=sqrt((sum1Sq-pow(sum1,2)/len(v1))*(sum2Sq-pow(sum2,2)/len(v1))) if den==0: return 0 return 1.0-num/den class bicluster: def __init__(self,vec,left=None,right=None,distance=0.0,id=None): self.left=left self.right=right self.vec=vec self.id=id self.distance=distance def hcluster(rows,distance=pearson): distances={} currentclustid=-1 # Clusters are initially just the rows clust=[bicluster(rows[i],id=i) for i in range(len(rows))] while len(clust)>1: lowestpair=(0,1) closest=distance(clust[0].vec,clust[1].vec) # loop through every pair looking for the smallest distance for i in range(len(clust)): for j in range(i+1,len(clust)): # distances is the cache of distance calculations if (clust[i].id,clust[j].id) not in distances: distances[(clust[i].id,clust[j].id)]=distance(clust[i].vec,clust[j].vec) d=distances[(clust[i].id,clust[j].id)] if d0: for rowid in bestmatches[i]: for m in range(len(rows[rowid])): avgs[m]+=rows[rowid][m] for j in range(len(avgs)): avgs[j]/=len(bestmatches[i]) clusters[i]=avgs return bestmatches def tanamoto(v1,v2): c1,c2,shr=0,0,0 for i in range(len(v1)): if v1[i]!=0: c1+=1 # in v1 if v2[i]!=0: c2+=1 # in v2 if v1[i]!=0 and v2[i]!=0: shr+=1 # in both return 1.0-(float(shr)/(c1+c2-shr)) def scaledown(data,distance=pearson,rate=0.01): n=len(data) # The real distances between every pair of items realdist=[[distance(data[i],data[j]) for j in range(n)] for i in range(0,n)] # Randomly initialize the starting points of the locations in 2D loc=[[random.random(),random.random()] for i in range(n)] fakedist=[[0.0 for j in range(n)] for i in range(n)] lasterror=None for m in range(0,1000): # Find projected distances for i in range(n): for j in range(n): fakedist[i][j]=sqrt(sum([pow(loc[i][x]-loc[j][x],2) for x in range(len(loc[i]))])) # Move points grad=[[0.0,0.0] for i in range(n)] totalerror=0 for k in range(n): for j in range(n): if j==k: continue # The error is percent difference between the distances errorterm=(fakedist[j][k]-realdist[j][k])/realdist[j][k] # Each point needs to be moved away from or towards the other # point in proportion to how much error it has grad[k][0]+=((loc[k][0]-loc[j][0])/fakedist[j][k])*errorterm grad[k][1]+=((loc[k][1]-loc[j][1])/fakedist[j][k])*errorterm # Keep track of the total error totalerror+=abs(errorterm) print totalerror # If the answer got worse by moving the points, we are done if lasterror and lasterror