## ----echo=F-------------------------------------------------------------------
set.seed(1)

## ----Load R packages----------------------------------------------------------

library(PAC)



## ----Load data----------------------------------------------------------------
sampleIDs<-c("Basal", "BCR", "IL7")


## ----PAC and Network Inference------------------------------------------------
samplePass(sampleIDs, dim_subset=NULL, hyperrectangles=35, num_PACSupop=25, num_networkEdge=25, max.iter=50)

## ----MAN----------------------------------------------------------------------

clades_network_only<-MAN(sampleIDs, num_PACSupop=25, smallSubpopCutoff=100, k_clades=5)


## ----refine PAC labels with MAN clade results---------------------------------
refineSubpopulationLabels(sampleIDs,dim_subset=NULL, clades_network_only, expressionGroupClamp=5)

## ----Clade Networks-----------------------------------------------------------
getRepresentativeNetworks(sampleIDs, dim_subset=NULL, SubpopSizeFilter=200, num_networkEdge=25)

## ----Annotation---------------------------------------------------------------
aggregateMatrix_withAnnotation<-annotateClades(sampleIDs, topHubs=4)
head(aggregateMatrix_withAnnotation)


## ----Append subpopulation proporation for each sample-------------------------
annotationMatrix_prop<-annotationMatrix_withSubpopProp(aggregateMatrix_withAnnotation)
head(annotationMatrix_prop)