singleCellNet: cell identity from single cell RNA-Seq data

# Patrick Cahan (C) 2017
# patrick.cahan@gmail.com


#' @export
sc_statTab<-function# make a gene stats table (i.e. alpha, mu, etc)
(expDat, # expression matrix
 dThresh=0 # threshold for detection
 ){
  
  statTab<-data.frame()
  muAll<-sc_compMu(expDat, threshold=dThresh);
  alphaAll<-sc_compAlpha(expDat,threshold=dThresh);
  meanAll<-apply(expDat, 1, mean);
  covAll<-apply(expDat, 1, sc_cov);
  fanoAll<-apply(expDat,1, sc_fano);
  maxAll<-apply(expDat, 1, max);
  sdAll<-apply(expDat, 1, sd);
  
  statTabAll<-data.frame(gene=rownames(expDat), mu=muAll, alpha=alphaAll, overall_mean=meanAll, cov=covAll, fano=fanoAll, max_val=maxAll, sd=sdAll)
  statTabAll;
}


# compute alpha given detection threshold
#' @export
sc_compAlpha<-function 
(expMat,
 threshold=0,
  pseudo=FALSE){
  
  indexFunction<-function(vector, threshold){
    names(which(vector>threshold));
  }
  
  indexes<-apply(expMat, 1, indexFunction, threshold);
  alphas<-unlist(lapply(indexes, length));
  ans<-alphas/ncol(expMat)
  if(pseudo){
    ans<-(alphas+1)/(ncol(expMat)+1)
  }
  ans
}

# compute Mu given threshold
#' @export
sc_compMu<-function 
(expMat,
 threshold=0){
  
  afunct<-function(vector, threshold){
    mean( vector[which(vector>threshold)] );
  } 
  
  mus<-unlist(apply(expMat, 1, afunct, threshold))
  mus[is.na(mus)]<-0;
  mus;
}

# replavce NAs with 0
repNA<-function
(vector){
  vector[which(is.na(vector))]<-0;
  vector;
}

#compute fano factor on vector
sc_fano<-function
(vector){
  var(vector)/mean(vector);
}

# compute coeef of variation on vector
sc_cov<-function
(vector){
  sd(vector)/mean(vector);
}


#' find genes that pass criteria
#'
#' based on idea that reliably detected genes will either be detected in many cells, or highly expressed in a small cels of cells (or both
#'
#' @param geneStats result of running sc_statTab
#' @param alpha1 proportion of cells in which a gene must be considered detected (as defined in geneStats)
#' @param alpha2 lower proportion of cells for genes that must have higher expression level
#' @param mu threshold, average expression level of genes passing the lower proportion criteria
#'
#' @return vector of gene symbols
#' 
#' @export
#'
sc_filterGenes<-function
(geneStats,
 alpha1=0.1,
 alpha2=0.01,
 mu=2){
	passing1<-rownames(geneStats[geneStats$alpha>alpha1,])
	notPassing<-setdiff(rownames(geneStats), passing1)
	geneStats<-geneStats[notPassing,]
	c(passing1, rownames(geneStats[which(geneStats$alpha>alpha2 & geneStats$mu>mu),]))
}


#' find cells that pass criteria
#'
#' based purely on umis
#'
#' @param sampTab, which must have UMI column
#' @param minVal umis must exceed this
#' @param maxValQuant quantile to select max threshold
#'
#' @return vector rownames(sampTab) meeting criteria
#' 
#' @export
#'
sc_filterCells<-function
(sampTab,
 minVal=1e3,
 maxValQuant=0.95){
	stX<-sampTab[sampTab$umis>minVal,]
	qThresh<-quantile(sampTab$umis, maxValQuant)
	rownames(stX[stX$umis<qThresh,])
}




#' finds genes higher in one group vs others
#'
#' finds genes higher in one group vs others
#'
#' @param expDat expression matrix
#' @param list of cells in eahc groupsampTab result of running cutreeDynamicTree 
#' @param dLevel dLevel
#'
#' @return list of grps -> names
#' 
#' @export
#'
sc_findEnr<-function 
(expDat,
 sampTab,
 dLevel="group")
{
  groups<-unique(as.vector(sampTab[,dLevel]))
  myMeans<-matrix(0,nrow=nrow(expDat), ncol=length(groups))
  rownames(myMeans)<-rownames(expDat)
  colnames(myMeans)<-groups

  for(group in groups){
    xi<-which(sampTab[,dLevel]==group)
    myMeans[,group]<-apply(expDat[,xi], 1, median)
  }

  ans<-list()
  for(group in groups){
    cat(group,"\n")
    others<-setdiff(groups, group)
    tmpMeans<-apply(myMeans[,others], 1, median)
    myDiff<-myMeans[,group] - tmpMeans
    ans[[group]]<-rownames(expDat)[order(myDiff, decreasing=TRUE)]
  }
  ans;
}

#' @export
enrDiff<-function 
(expDat,
 sampTab,
 dLevel="group")
{
  groups<-unique(as.vector(sampTab[,dLevel]))
  myMeans<-matrix(0,nrow=nrow(expDat), ncol=length(groups))
  rownames(myMeans)<-rownames(expDat)
  colnames(myMeans)<-groups

  for(group in groups){
    xi<-which(sampTab[,dLevel]==group)
    myMeans[,group]<-apply(expDat[,xi], 1, median)
  }

  ans<-matrix(0,nrow=nrow(expDat), ncol=length(groups))
  colnames(ans)<-groups
  rownames(ans)<-rownames(expDat)
  for(group in groups){
    cat(group,"\n")
    others<-setdiff(groups, group)
    tmpMeans<-apply(myMeans[,others], 1, median)
    myDiff<-myMeans[,group] - tmpMeans
    ans[,group]<-myDiff
  }
  ans
}



### bins genes into x groups based on overallmean
binGenesAlpha<-function
(geneStats,
 nbins=20){
  max<-max(geneStats$alpha);
  min<-min(geneStats$alpha);

  binGroup<-rep(nbins, length=nrow(geneStats));
  names(binGroup)<-rownames(geneStats);
  rrange<-max-min;
  inc<-rrange/nbins
  borders<-seq(inc, max, by=inc)
  for(i in length(borders):1){
    xnames<-rownames(geneStats[which(geneStats$alpha<=borders[i]),]);
    binGroup[xnames]<-i;
  }
  cbind(geneStats, bin=binGroup);
}

### bins genes into x groups based on overallmean
binGenes<-function
(geneStats,
 nbins=20,
 meanType="overall_mean"){

##  max<-max(geneStats$overall_mean);
##  min<-min(geneStats$overall_mean);

  max<-max(geneStats[,meanType])
  min<-min(geneStats[,meanType])

  binGroup<-rep(nbins, length=nrow(geneStats));
  names(binGroup)<-rownames(geneStats);
  rrange<-max-min;
  inc<-rrange/nbins
  borders<-seq(inc, max, by=inc)
  for(i in length(borders):1){
    #xnames<-rownames(geneStats[which(geneStats$overall_mean<=borders[i]),]);
    xnames<-rownames(geneStats[which(geneStats[,meanType]<=borders[i]),]);
    binGroup[xnames]<-i;
  }
  cbind(geneStats, bin=binGroup);
}

# find most variable genes
#' @export
findVarGenes<-function
(expNorm,
  geneStats,
  zThresh=2, 
  meanType="overall_mean"){
  allGenes<-rownames(expNorm)
  sg<-binGenesAlpha(geneStats)
  zscs<-rep(0, nrow(sg));
  names(zscs)<-rownames(sg);
  bbins<-unique(sg$bin);
  for(bbin in bbins){
    xx<-sg[sg$bin==bbin,];
    tmpZ<-scale(xx$fano);
    zscs[ rownames(xx) ]<-tmpZ[,1];
  }

  zByAlpha<-names(which(zscs>zThresh))
  
  # by overall mean
  sg<-binGenes(geneStats, meanType=meanType)
  zscsM<-rep(0, nrow(sg));
  names(zscsM)<-rownames(sg);
  bbins<-unique(sg$bin);
  for(bbin in bbins){
    xx<-sg[sg$bin==bbin,];
    tmpZ<-scale(xx$fano);
    zscsM[ rownames(xx) ]<-tmpZ[,1];
  }
  zByMean<-names(which(zscsM>zThresh))

  # by mu
  sg<-binGenes(geneStats, meanType="mu")
  zscsM<-rep(0, nrow(sg));
  names(zscsM)<-rownames(sg);
  bbins<-unique(sg$bin);
  for(bbin in bbins){
    xx<-sg[sg$bin==bbin,];
    ###tmpZ<-scale(xx$fano);
    tmpZ<-scale(xx$cov);
    zscsM[ rownames(xx) ]<-tmpZ[,1];
  }
  zByMu<-names(which(zscsM>zThresh))


  union(zByMu,union(zByMean, zByAlpha))

}



par_findSpecGenes<-function#
(expDat, ### expression matrix
  sampTab, ### sample tableß
  ###holm=1e-50, ### sig threshold
  ###cval=0.5, ### R thresh
  dLevel="group", #### annotation level to group on
  prune=FALSE, ### limit to genes exclusively detected as CT in one CT
  minSet=TRUE,
  ncore=4
){

  newST<-sampTab
  if(minSet){
    cat("Making reduced sampleTable\n")
    newST<-minTab(sampTab, dLevel)
  }
  
  ans<-list()

  cat("Making patterns\n")
  myPatternG<-sc_sampR_to_pattern(as.vector(newST[,dLevel]));
  expDat<-expDat[,rownames(newST)]
  
  cat("Testing patterns\n")
 # aClust<-parallel::makeCluster(ncore, type='FORK')
  specificSets<-lapply(myPatternG, sc_testPattern, expDat=expDat)
 # stopCluster(aClust)
  cat("Done testing\n")

  if(prune){
  # now limit to genes exclusive to each list
   specGenes<-list();
   for(ctName in ctNames){
     others<-setdiff(ctNames, ctName);
     x<-setdiff( ctGenes[[ctName]], unlist(ctGenes[others]));
     specGenes[[ctName]]<-x;
   }
   ans<-specGenes;
  }
  else{
   ans<-specificSets
  }
###  names(ans)<-as.character(ctNames)
  ans
}


#' @export
sc_sampR_to_pattern<-function#
(sampR){
  d_ids<-unique(as.vector(sampR));
  nnnc<-length(sampR);
#  ans<-matrix(nrow=length(d_ids), ncol=nnnc);
  ans<-list()
  for(d_id in d_ids){
    x<-rep(0,nnnc);
    x[which(sampR==d_id)]<-1;
    ans[[d_id]]<-x;
  }
  ans
}



#' @export
sc_testPatternTrans<-function(pattern, expDat){
  pval<-vector();
  cval<-vector();
  geneids<-colnames(expDat);
  llfit<-ls.print(lsfit(pattern, expDat), digits=25, print=FALSE);
  xxx<-matrix( unlist(llfit$coef), ncol=8,byrow=TRUE);
  ccorr<-xxx[,6];
  cval<- sqrt(as.numeric(llfit$summary[,2])) * sign(ccorr);
  pval<-as.numeric(xxx[,8]);

  #qval<-qvalue(pval)$qval;
  holm<-p.adjust(pval, method='holm');
  #data.frame(row.names=geneids, pval=pval, cval=cval, qval=qval, holm=holm);
  data.frame(row.names=geneids, pval=pval, cval=cval,holm=holm);
}

#' @export
sc_testPattern<-function(pattern, expDat){
  pval<-vector();
  cval<-vector();
  geneids<-rownames(expDat);
  llfit<-ls.print(lsfit(pattern, t(expDat)), digits=25, print=FALSE);
  xxx<-matrix( unlist(llfit$coef), ncol=8,byrow=TRUE);
  ccorr<-xxx[,6];
  cval<- sqrt(as.numeric(llfit$summary[,2])) * sign(ccorr);
  pval<-as.numeric(xxx[,8]);

  #qval<-qvalue(pval)$qval;
  holm<-p.adjust(pval, method='holm');
  #data.frame(row.names=geneids, pval=pval, cval=cval, qval=qval, holm=holm);
  data.frame(row.names=geneids, pval=pval, cval=cval,holm=holm);
}



#' @export
getTopGenes<-function
(xdat,
  topN=3)
# cval=.35,
# holm=1e-2)
{
#  qqq<-xdat[which(xdat$cval>cval & xdat$holm<holm),]
#  rownames(qqq[order(qqq$cval, decreasing=TRUE),][1:topN,])
  rownames(xdat[order(xdat$cval, decreasing=TRUE),][1:topN,])
}

#' get the genes specific to each diffexp in a list of them
#'
#' get the genes specific to each diffexp in a list of them
#'
#' @param xdatList list of diffexp data frame, must have cval column
#' @param topN 50 numb of genes to return per diffexp
#'
#' @return named list of genes
#' 
#' @export
getSpecGenes<-function
(xdatList,
  topN=50)
{
  tmpAns<-lapply(xdatList, getTopGenes, topN=topN)
  allgenes<-unique(unlist(tmpAns))
  ans<-list()
  cnames<-names(tmpAns)
  for(cname in cnames){
    a<-tmpAns[[cname]]
    others<-setdiff(cnames, cname)
    b<-unique(unlist(tmpAns[others]))
    ans[[cname]]<-setdiff(a, b)
  }
  ans
}




#' @export
getTopGenesList<-function
(gpaResSortOf,
  topN=3)
# cval=.35,
# holm=1e-2)
{

  gnames<-names(gpaResSortOf$diffExp)
  tmpAns<-vector()
  for(gname in gnames){
    tmpAns<-append(tmpAns, paste( getTopGenes(gpaResSortOf$diffExp[[gname]], topN), collapse=", "))
  }
  names(tmpAns)<-gnames
  tmpAns
}


minTab<-function #subsample the table
(sampTab, dLevel){
  myMin<-min(table(sampTab[,dLevel]))
  nST<-data.frame()
  grps<-unique(as.vector(sampTab[,dLevel]))
  for(grp in grps){
    stX<-sampTab[sampTab[,dLevel]==grp,]
    nST<-rbind(nST, stX[sample(rownames(stX), myMin),])
  }
  nST
}