Nothing
## ---- 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)
## ----Heatmap input and plot heatmap--------------------------------------
cladeProportionMatrix<-heatmapInput(aggregateMatrix_withAnnotation)
heatmap(as.matrix(cladeProportionMatrix))
## ----Append subpopulation proporation for each sample--------------------
annotationMatrix_prop<-annotationMatrix_withSubpopProp(aggregateMatrix_withAnnotation)
head(annotationMatrix_prop)
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