## ----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())