plotFemap {fedup} | R Documentation

## Draws a network representation of overlaps among pathway enrichment results using EnrichmentMap (EM) in Cytoscape.

### Description

Draws a network representation of overlaps among pathway enrichment results using EnrichmentMap (EM) in Cytoscape.

### Usage

    plotFemap(
        gmtFile,
        resultsFolder,
        pvalue = 1,
        qvalue = 1,
        formSim = "COMBINED",
        edgeSim = 0.375,
        combSim = 0.5,
        chartData = "NES_VALUE",
        clustAlg = "MCL",
        clustWords = 3,
        hideNodeLabels = FALSE,
        netName = "generic",
        netFile = "png"
    )

### Arguments

`gmtFile` | (char) absolute path to GMT file (generated via writePathways)
`resultsFolder` | (char) absolute path to folder with fedup results (generated via writeFemap)
`pvalue` | (numeric) pvalue cutoff (value between 0 and 1; default 1)
`qvalue` | (numeric) qvalue cutoff (value between 0 and 1; default 1)
`formSim` | (character) formula to calculate similarity score (one of OVERLAP, JACCARD, COMBINED; default COMBINED)
`edgeSim` | (numeric) edge similarity score cutoff (value between 0 and 1; default 0.375)
`combSim` | (numeric) when coefficients=COMBINED this parameter is used to determine what percentage to use for JACCARD and OVERLAP when combining their value (value between 0 to 1; default 0.5)
`chartData` | (char) node chart data (one of NES_VALUE, P_VALUE, FDR_VALUE, PHENOTYPES, DATA_SET, EXPRESSION_SET, or NONE; default NES_VALUE)
`clustAlg` | (character) clusterMaker algorith (one of AFFINITY_PROPAGATION, CLUSTER_FIZZIFIER, GLAY, CONNECTED_COMPONENTS, MCL, SCPS; default MCL)
`clustWords` | (integer) maximum words to include in autoAnnotate cluster label (default 3)
`hideNodeLabels` | (logical) if TRUE hides the node label in the EM; cluster labels generated via AutoAnnotate remain visible
`netName` | (char) name for EM in Cytoscape (default generic)
`netFile` | (char) name of output image (supports png, pdf, svg, jpeg image formats)

### Value

File name of image to which the network is exported and an open session of Cytoscape (side effect of plotting EM). NULL if Cytoscape is not running locally.

### Examples

    # Load example data
    data(geneDouble)
    data(pathwaysGMT)
    # Run fedup
    fedupRes <- runFedup(geneDouble, pathwaysGMT)
    # Write out results to temp folder
    resultsFolder <- tempdir()
    writeFemap(fedupRes, resultsFolder)
    # Write out gmt formatted pathawy annotations to temp file
    gmtFile <- tempfile("pathwaysGMT", fileext = ".gmt")
    writePathways(pathwaysGMT, gmtFile)
    # Plot enrichment map
    netFile <- tempfile("fedup_EM", fileext = ".png")
    plotFemap(
        gmtFile = gmtFile,
        resultsFolder = resultsFolder,
        qvalue = 0.05,
        hideNodeLabels = TRUE,
        netName = "fedup_EM",
        netFile = netFile
    )

[Package fedup version 1.2.0 Index]