plotFemap {fedup} | R Documentation |
Draws a network representation of overlaps among pathway enrichment results using EnrichmentMap (EM) in Cytoscape.
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" )
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) |
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.
# 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 )