In hfang-bristol/XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

knitr::opts_chunk$set(results="asis")
knitr::opts_chunk$set(cache=FALSE)
knitr::opts_chunk$set(echo=FALSE)
knitr::opts_chunk$set(warning=FALSE)
knitr::opts_chunk$set(message=FALSE)
knitr::opts_chunk$set(fig_cap="yes")

Overview

This fully self-contained report consists of tables and plots for you exploring results, with both text and pdf files downloadable (also embedded inside for the unrestricted sharing).

Results {.tabset .tabset-fade .tabset-pills}

Table

df_enrichment <- xEnrichViewer(obj, top_num="all", details=T)[, c('name','zscore',"pvalue",'adjp','or',"CIl","CIu","nOverlap","members_Overlap")]

# text file for download
tmpfile <- paste0(tempfile(), '.txt')
write.table(df_enrichment, file=tmpfile, sep="\t", row.names=FALSE)
hlink_txt <- xAuxEmbed(tmpfile, link.text="Download TEXT")

List of enrichments (r hlink_txt)

df_enrichment <- subset(df_enrichment, adjp<0.05)[,c(1:7)]

## only for AA pathway
if(eTerm$g$ontology %in% "AA"){

    if(0){
    df_enrichment$download <- sapply(rownames(df_enrichment), function (x){
        sprintf("<a href='http://galahad.well.ox.ac.uk:3030/A2/explorer/%s' target='%s''>%s</a>", x, x, x)
    })
    }

    data <- data.frame(label=eTerm$data, lfc=1, stringsAsFactors=F)

    vec_outfile <- sapply(rownames(df_enrichment), function(query){
        out.file <- paste0(tempfile(), ".", query, '.graphml')
        xGraphML2AA(data=data, query=query, node.label="label", node.color="lfc", colormap="white-orange", filename=out.file, RData.location=RData.location, verbose=F)
        out.file
    })

    df_enrichment$download <- sapply(vec_outfile, function(x){
        download.attribute <- paste0(names(x), '.graphml')
        hlink_graphml <- xAuxEmbed(x, download.attribute=download.attribute, link.text="GraphML")
    })

}

DT::datatable(df_enrichment, options=list(pageLength=5), style='default', caption="", rownames=FALSE, escape=F)

Plot

## only for AA pathway
if(eTerm$g$ontology %in% "AA"){
    AA.template <- xRDataLoader("AA.template", verbose=F, RData.location=RData.location)
    # consensus tree
    ig <- AA.template$consensus$ig
}else{
    ig <- NULL
}

gp <- xEnrichGGraph(obj, ig=ig)

# pdf file for download
tmpfile <- paste0(tempfile(), '.pdf')
pdf(file=tmpfile)
print(gp)
graphics.off()
hlink_pdf <- xAuxEmbed(tmpfile, link.text="Download PDF")

Plot of enrichments (r hlink_pdf)

gp

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.