## ----bgee1, echo=TRUE, eval=FALSE, warning=FALSE, fig.width = 7, fig.height = 7, fig.align='center'----
#  library(RITANdata)
#  library(RITAN)
#  library(BgeeDB)
#  bgee <- Bgee$new(species = "Homo_sapiens", dataType = "rna_seq", release = "13.2")
#  data <- getData(bgee)
#  
#  e <- formatData(bgee, data[[1]], callType = "present", stats = "rpkm")
#  # str(sampleNames(e))
#  # str(featureNames(e))
#  # str(phenoData(e))
#  # table(phenoData(e)@data$Anatomical.entity.name)
#  
#  ## -------------------- -
#  ## Get expression in two tissues
#  tmp <- exprs(e)[ , phenoData(e)@data$Anatomical.entity.name == "heart" ]
#  i <- apply( tmp, 1, function(x){ any(is.na(x)) })
#  expr_heart <- tmp[ !i, ]
#  
#  tmp <- exprs(e)[ , phenoData(e)@data$Anatomical.entity.name == "skeletal muscle tissue" ]
#  i <- apply( tmp, 1, function(x){ any(is.na(x)) })
#  expr_skele <- tmp[ !i, ]
#  
#  library(venn)
#  venn::venn( list(Heart = rownames(expr_heart),
#                   Skeletal = rownames(expr_skele) ),
#              cexil= 1, cexsn = 1, zcolor = "style" )
#  
#  ## -------------------- -
#  library(biomaRt)
#  ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl" )
#  map_heart <- getBM( attributes=c('ensembl_gene_id','ensembl_transcript_id','hgnc_symbol'),
#                      filters = 'ensembl_gene_id', values = rownames(expr_heart), mart = ensembl )
#  map_skele <- getBM( attributes=c('ensembl_gene_id','ensembl_transcript_id','hgnc_symbol'),
#                      filters = 'ensembl_gene_id', values = rownames(expr_skele), mart = ensembl )
#  
#  ## -------------------- -
#  ## Enrichment Within Each Tissue
#  
#  to do...
#  
#  
#  ## -------------------- -
#  ## Network Interactions Within Each Tissue
#  
#  to do...
#  
#  
#  ## -------------------- -
#  ## Similarities and Differences Between Tissues
#  
#  to do...
#  
#  
#