## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  echo = TRUE,
  message = FALSE,
  warning = FALSE,
  fig.width=8, fig.height=5
)

## ----eval=TRUE----------------------------------------------------------------
library(TissueEnrich)
genes<-system.file("extdata", "inputGenes.txt", package = "TissueEnrich")
inputGenes<-scan(genes,character())
gs<-GeneSet(geneIds=inputGenes,organism="Homo Sapiens",geneIdType=SymbolIdentifier())
output<-teEnrichment(inputGenes = gs)

## ----eval=TRUE----------------------------------------------------------------
seEnrichmentOutput<-output[[1]]
enrichmentOutput<-setNames(data.frame(assay(seEnrichmentOutput),row.names = rowData(seEnrichmentOutput)[,1]), colData(seEnrichmentOutput)[,1])
enrichmentOutput$Tissue<-row.names(enrichmentOutput)
head(enrichmentOutput)
ggplot(enrichmentOutput,aes(x=reorder(Tissue,-Log10PValue),y=Log10PValue,label = Tissue.Specific.Genes,fill = Tissue))+
      geom_bar(stat = 'identity')+
      labs(x='', y = '-LOG10(P-Adjusted)')+
      theme_bw()+
      theme(legend.position="none")+
      theme(plot.title = element_text(hjust = 0.5,size = 20),axis.title = element_text(size=15))+
      theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1),panel.grid.major= element_blank(),panel.grid.minor = element_blank())

## ----eval=TRUE----------------------------------------------------------------
ggplot(enrichmentOutput,aes(x=reorder(Tissue,-fold.change),y=fold.change,label = Tissue.Specific.Genes,fill = Tissue))+
      geom_bar(stat = 'identity')+
      labs(x='', y = 'Fold change')+
      theme_bw()+
      theme(legend.position="none")+
      theme(plot.title = element_text(hjust = 0.5,size = 20),axis.title = element_text(size=15))+
      theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1),panel.grid.major= element_blank(),panel.grid.minor = element_blank())

## ----eval=TRUE----------------------------------------------------------------
library(tidyr)
seExp<-output[[2]][["Placenta"]]
exp<-setNames(data.frame(assay(seExp), row.names = rowData(seExp)[,1]), colData(seExp)[,1])
exp$Gene<-row.names(exp)
exp<-exp %>% gather(key = "Tissue", value = "expression",1:(ncol(exp)-1))

ggplot(exp, aes(Tissue, Gene)) + geom_tile(aes(fill = expression),
     colour = "white") + scale_fill_gradient(low = "white",
     high = "steelblue")+
     labs(x='', y = '')+
      theme_bw()+
      guides(fill = guide_legend(title = "Log2(TPM)"))+
      #theme(legend.position="none")+
      theme(plot.title = element_text(hjust = 0.5,size = 20),axis.title = element_text(size=15))+
      theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1),panel.grid.major= element_blank(),panel.grid.minor = element_blank())


## ----eval=TRUE----------------------------------------------------------------
seGroupInf<-output[[3]][["Placenta"]]
groupInf<-data.frame(assay(seGroupInf))
print(head(groupInf))

## ----eval=TRUE----------------------------------------------------------------
print(geneIds(output[[4]]))

## ----eval=TRUE----------------------------------------------------------------
library(TissueEnrich)
library(ggplot2)
genes<-system.file("extdata", "inputGenes.txt", package = "TissueEnrich")
inputGenes<-scan(genes,character())
gs<-GeneSet(geneIds=inputGenes,organism="Homo Sapiens",geneIdType=SymbolIdentifier())
output<-teEnrichment(inputGenes = gs,rnaSeqDataset = 3)
seEnrichmentOutput<-output[[1]]
enrichmentOutput<-setNames(data.frame(assay(seEnrichmentOutput), row.names = rowData(seEnrichmentOutput)[,1]), colData(seEnrichmentOutput)[,1])
enrichmentOutput$Tissue<-row.names(enrichmentOutput)
ggplot(enrichmentOutput,aes(x=reorder(Tissue,-Log10PValue),y=Log10PValue,label = Tissue.Specific.Genes,fill = Tissue))+
      geom_bar(stat = 'identity')+
      labs(x='', y = '-LOG10(P-Adjusted)')+
      theme_bw()+
      theme(legend.position="none")+
      theme(plot.title = element_text(hjust = 0.5,size = 20),axis.title = element_text(size=15))+
      theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1),panel.grid.major= element_blank(),panel.grid.minor = element_blank())

## ----eval=TRUE----------------------------------------------------------------
library(TissueEnrich)
library(SummarizedExperiment)
data<-system.file("extdata", "test.expressiondata.txt", package = "TissueEnrich")
expressionData<-read.table(data,header=TRUE,row.names=1,sep='\t')
se<-SummarizedExperiment(assays = SimpleList(as.matrix(expressionData)),rowData = row.names(expressionData),colData = colnames(expressionData))
output<-teGeneRetrieval(se)
head(assay(output))

## ----eval=FALSE---------------------------------------------------------------
#  library(TissueEnrich)
#  library(ggplot2)
#  genes<-system.file("extdata", "inputGenesEnsembl.txt", package = "TissueEnrich")
#  inputGenes<-scan(genes,character())
#  gs<-GeneSet(geneIds=inputGenes)
#  output2<-teEnrichmentCustom(gs,output)
#  enrichmentOutput<-setNames(data.frame(assay(output2[[1]]), row.names = rowData(output2[[1]])[,1]), colData(output2[[1]])[,1])
#  ggplot(enrichmentOutput,aes(x=reorder(Tissue,-Log10PValue),y=Log10PValue,label = Tissue.Specific.Genes,fill = Tissue))+
#        geom_bar(stat = 'identity')+
#        labs(x='', y = '-LOG10(P-Adjusted)')+
#        theme_bw()+
#        theme(legend.position="none")+
#        theme(plot.title = element_text(hjust = 0.5,size = 20),axis.title = element_text(size=15))+
#        theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1),panel.grid.major= element_blank(),panel.grid.minor = element_blank())

