Examples with EMCreationParameters org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters used on opensource projects

Example 21 with EMCreationParameters

use of org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters in project EnrichmentMapApp by BaderLab.

the class HeatMapRanksTest method setUp.

@Before
public void setUp(EnrichmentMapManager emManager) {
    DataSetFiles files = new DataSetFiles();
    files.setGMTFileName(PATH + "Human_GO_AllPathways_no_GO_iea_April_15_2013_symbol.gmt");
    files.setExpressionFileName(PATH + "MCF7_ExprMx_v2_names.gct");
    files.setEnrichmentFileName1(PATH + "gsea_report_for_ES12_1473194913081.xls");
    files.setEnrichmentFileName2(PATH + "gsea_report_for_NT12_1473194913081.xls");
    files.setRankedFile(PATH + "ranked_gene_list_ES12_versus_NT12_1473194913081.xls");
    files.setClassFile(PATH + "ES_NT.cls");
    EMCreationParameters params = new EMCreationParameters("HeatMapRanks_", 0.005, 0.1, NESFilter.ALL, Optional.empty(), SimilarityMetric.OVERLAP, 0.5, 0.5);
    Map<Long, EnrichmentMap> maps = emManager.getAllEnrichmentMaps();
    assertEquals(0, maps.size());
    buildEnrichmentMap(params, files, Method.GSEA, LegacySupport.DATASET1);
    maps = emManager.getAllEnrichmentMaps();
    assertEquals(1, maps.size());
}