Nothing
## ----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())
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