diff --git a/components/00SourceAll.R b/components/00SourceAll.R index 4f9221ef9..5f15e55a1 100644 --- a/components/00SourceAll.R +++ b/components/00SourceAll.R @@ -1,250 +1,250 @@ ## Generated automatically: do not edit by hand -message("source all called from wd = ", getwd()) -if (!file.exists("00SourceAll.R")) { - message("WARNING: not in source folder. skipping.") +message('source all called from wd = ',getwd()) +if(!file.exists('00SourceAll.R')) { + message('WARNING: not in source folder. skipping.') } else { - message("Note: sourcing all code...") - source("app/R/utils/auth.R", encoding = "UTF-8") - source("app/R/utils/database.R", encoding = "UTF-8") - source("app/R/utils/open_url.R", encoding = "UTF-8") - source("app/R/utils/utils.R", encoding = "UTF-8") - source("board.biomarker/R/biomarker_plot_boxplots.R", encoding = "UTF-8") - source("board.biomarker/R/biomarker_plot_decisiontree.R", encoding = "UTF-8") - source("board.biomarker/R/biomarker_plot_featurerank.R", encoding = "UTF-8") - source("board.biomarker/R/biomarker_plot_heatmap.R", encoding = "UTF-8") - source("board.biomarker/R/biomarker_plot_importance.R", encoding = "UTF-8") - source("board.biomarker/R/biomarker_server.R", encoding = "UTF-8") - source("board.biomarker/R/biomarker_ui.R", encoding = "UTF-8") - source("board.clustering/R/clustering_plot_clustannot.R", encoding = "UTF-8") - source("board.clustering/R/clustering_plot_clusterpca.R", encoding = "UTF-8") - source("board.clustering/R/clustering_plot_genemodule.R", encoding = "UTF-8") - source("board.clustering/R/clustering_plot_phenoplot.R", encoding = "UTF-8") - source("board.clustering/R/clustering_plot_splitmap.R", encoding = "UTF-8") - source("board.clustering/R/clustering_plot_table_parcoord.R", encoding = "UTF-8") - source("board.clustering/R/clustering_server.R", encoding = "UTF-8") - source("board.clustering/R/clustering_table_clustannot.R", encoding = "UTF-8") - source("board.clustering/R/clustering_ui.R", encoding = "UTF-8") - source("board.compare/R/compare_plot_compare1.R", encoding = "UTF-8") - source("board.compare/R/compare_plot_compare2.R", encoding = "UTF-8") - source("board.compare/R/compare_plot_cum_fc1.R", encoding = "UTF-8") - source("board.compare/R/compare_plot_cum_fc2.R", encoding = "UTF-8") - source("board.compare/R/compare_plot_expression.R", encoding = "UTF-8") - source("board.compare/R/compare_plot_fcfc.R", encoding = "UTF-8") - source("board.compare/R/compare_plot_genecorr.R", encoding = "UTF-8") - source("board.compare/R/compare_server.R", encoding = "UTF-8") - source("board.compare/R/compare_table_corr_score.R", encoding = "UTF-8") - source("board.compare/R/compare_ui.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_plot_connectivityHeatmap.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_plot_connectivityMap.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_plot_cumEnrichmentPlot.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_plot_cumFCplot.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_plot_enrichmentGraph.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_plot_FCFCplots.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_plot_leadingEdgeGraph.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_plot_scatterPlot.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_server.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_table_foldchange.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_table_similarity_scores.R", encoding = "UTF-8") - source("board.connectivity/R/connectivity_ui.R", encoding = "UTF-8") - source("board.correlation/R/correlation_plot_barplot.R", encoding = "UTF-8") - source("board.correlation/R/correlation_plot_cor_graph.R", encoding = "UTF-8") - source("board.correlation/R/correlation_plot_correlation_UMAP.R", encoding = "UTF-8") - source("board.correlation/R/correlation_plot_scattercorr.R", encoding = "UTF-8") - source("board.correlation/R/correlation_server.R", encoding = "UTF-8") - source("board.correlation/R/correlation_table_corr.R", encoding = "UTF-8") - source("board.correlation/R/correlation_ui.R", encoding = "UTF-8") - source("board.dataview/R/dataview_module_geneinfo.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_abundance.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_averagecounts.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_averagerank.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_boxplot.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_correlation.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_expression.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_genetypes.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_histogram.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_phenoassociation.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_phenoheatmap.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_tissue.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_totalcounts.R", encoding = "UTF-8") - source("board.dataview/R/dataview_plot_tsneplot.R", encoding = "UTF-8") - source("board.dataview/R/dataview_server.R", encoding = "UTF-8") - source("board.dataview/R/dataview_table_contrasts.R", encoding = "UTF-8") - source("board.dataview/R/dataview_table_rawdata.R", encoding = "UTF-8") - source("board.dataview/R/dataview_table_samples.R", encoding = "UTF-8") - source("board.dataview/R/dataview_ui.R", encoding = "UTF-8") - source("board.drugconnectivity/R/drugconnectivity_plot_actmap.R", encoding = "UTF-8") - source("board.drugconnectivity/R/drugconnectivity_plot_cmap_dsea.R", encoding = "UTF-8") - source("board.drugconnectivity/R/drugconnectivity_plot_cmap_enplot.R", encoding = "UTF-8") - source("board.drugconnectivity/R/drugconnectivity_plot_enplots.R", encoding = "UTF-8") - source("board.drugconnectivity/R/drugconnectivity_plot_moa.R", encoding = "UTF-8") - source("board.drugconnectivity/R/drugconnectivity_server.R", encoding = "UTF-8") - source("board.drugconnectivity/R/drugconnectivity_table_cmap.R", encoding = "UTF-8") - source("board.drugconnectivity/R/drugconnectivity_table_dsea.R", encoding = "UTF-8") - source("board.drugconnectivity/R/drugconnectivity_ui.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_plot_barplot.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_plot_compare.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_plot_freq_top_gsets.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_plot_geneplot.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_plot_scatter.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_plot_top_enrich_gsets.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_plot_volcano.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_plot_volcanoall.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_plot_volcanomethods.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_server.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_table_enrichment_analysis.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_table_genes_in_geneset.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_table_gset_enrich_all_contrasts.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_table_n_sig_gsets.R", encoding = "UTF-8") - source("board.enrichment/R/enrichment_ui.R", encoding = "UTF-8") - source("board.expression/R/expression_plot_barplot.R", encoding = "UTF-8") - source("board.expression/R/expression_plot_maplot.R", encoding = "UTF-8") - source("board.expression/R/expression_plot_topfoldchange.R", encoding = "UTF-8") - source("board.expression/R/expression_plot_topgenes.R", encoding = "UTF-8") - source("board.expression/R/expression_plot_volcano.R", encoding = "UTF-8") - source("board.expression/R/expression_plot_volcanoAll.R", encoding = "UTF-8") - source("board.expression/R/expression_plot_volcanoMethods.R", encoding = "UTF-8") - source("board.expression/R/expression_server.R", encoding = "UTF-8") - source("board.expression/R/expression_table_fctable.R", encoding = "UTF-8") - source("board.expression/R/expression_table_FDRtable.R", encoding = "UTF-8") - source("board.expression/R/expression_table_genetable.R", encoding = "UTF-8") - source("board.expression/R/expression_table_gsettable.R", encoding = "UTF-8") - source("board.expression/R/expression_ui.R", encoding = "UTF-8") - source("board.featuremap/R/featuremap_plot_gene_sig.R", encoding = "UTF-8") - source("board.featuremap/R/featuremap_plot_gset_sig.R", encoding = "UTF-8") - source("board.featuremap/R/featuremap_plot_table_gene_map.R", encoding = "UTF-8") - source("board.featuremap/R/featuremap_plot_table_geneset_map.R", encoding = "UTF-8") - source("board.featuremap/R/featuremap_server.R", encoding = "UTF-8") - source("board.featuremap/R/featuremap_ui.R", encoding = "UTF-8") - source("board.intersection/R/intersection_plot_contrast_correlation.R", encoding = "UTF-8") - source("board.intersection/R/intersection_plot_foldchange_heatmap.R", encoding = "UTF-8") - source("board.intersection/R/intersection_plot_scatterplot_pairs.R", encoding = "UTF-8") - source("board.intersection/R/intersection_plot_table_venn_diagram.R", encoding = "UTF-8") - source("board.intersection/R/intersection_server.R", encoding = "UTF-8") - source("board.intersection/R/intersection_ui.R", encoding = "UTF-8") - source("board.loading/R/loading_module_received.R", encoding = "UTF-8") - source("board.loading/R/loading_module_shared.R", encoding = "UTF-8") - source("board.loading/R/loading_server.R", encoding = "UTF-8") - source("board.loading/R/loading_table_datasets_public.R", encoding = "UTF-8") - source("board.loading/R/loading_table_datasets.R", encoding = "UTF-8") - source("board.loading/R/loading_tsneplot.R", encoding = "UTF-8") - source("board.loading/R/loading_ui.R", encoding = "UTF-8") - source("board.loading/R/loading_utils.R", encoding = "UTF-8") - source("board.pathway/R/pathway_enrichmap.R", encoding = "UTF-8") - source("board.pathway/R/pathway_plot_enrichmap.R", encoding = "UTF-8") - source("board.pathway/R/pathway_plot_go_actmap.R", encoding = "UTF-8") - source("board.pathway/R/pathway_plot_go_network.R", encoding = "UTF-8") - source("board.pathway/R/pathway_plot_reactome_actmap.R", encoding = "UTF-8") - source("board.pathway/R/pathway_plot_reactome_graph.R", encoding = "UTF-8") - source("board.pathway/R/pathway_plot_wikipathway_actmap.R", encoding = "UTF-8") - source("board.pathway/R/pathway_plot_wikipathway_graph.R", encoding = "UTF-8") - source("board.pathway/R/pathway_server.R", encoding = "UTF-8") - source("board.pathway/R/pathway_table_go_table.R", encoding = "UTF-8") - source("board.pathway/R/pathway_table_reactome.R", encoding = "UTF-8") - source("board.pathway/R/pathway_table_wikipathway.R", encoding = "UTF-8") - source("board.pathway/R/pathway_ui.R", encoding = "UTF-8") - source("board.pathway/R/pathway_wikipathview.R", encoding = "UTF-8") - source("board.pcsf/R/pcsf_plot_heatmap.R", encoding = "UTF-8") - source("board.pcsf/R/pcsf_plot_network.R", encoding = "UTF-8") - source("board.pcsf/R/pcsf_server.R", encoding = "UTF-8") - source("board.pcsf/R/pcsf_table_centrality.R", encoding = "UTF-8") - source("board.pcsf/R/pcsf_ui.R", encoding = "UTF-8") - source("board.pcsf/R/util_pcsf.R", encoding = "UTF-8") - source("board.signature/R/signature_plot_enplots.R", encoding = "UTF-8") - source("board.signature/R/signature_plot_markers.R", encoding = "UTF-8") - source("board.signature/R/signature_plot_overlap.R", encoding = "UTF-8") - source("board.signature/R/signature_plot_volcano.R", encoding = "UTF-8") - source("board.signature/R/signature_server.R", encoding = "UTF-8") - source("board.signature/R/signature_table_enrich_by_contrasts.R", encoding = "UTF-8") - source("board.signature/R/signature_table_genes_in_signature.R", encoding = "UTF-8") - source("board.signature/R/signature_table_overlap.R", encoding = "UTF-8") - source("board.signature/R/signature_ui.R", encoding = "UTF-8") - source("board.singlecell/R/singlecell_plot_crosstabPlot.R", encoding = "UTF-8") - source("board.singlecell/R/singlecell_plot_cytoplot.R", encoding = "UTF-8") - source("board.singlecell/R/singlecell_plot_icpplot.R", encoding = "UTF-8") - source("board.singlecell/R/singlecell_plot_mappingplot.R", encoding = "UTF-8") - source("board.singlecell/R/singlecell_plot_markersplot.R", encoding = "UTF-8") - source("board.singlecell/R/singlecell_plot_phenoplot.R", encoding = "UTF-8") - source("board.singlecell/R/singlecell_server.R", encoding = "UTF-8") - source("board.singlecell/R/singlecell_ui.R", encoding = "UTF-8") - source("board.tcga/R/tcga_plot_survival.R", encoding = "UTF-8") - source("board.tcga/R/tcga_server.R", encoding = "UTF-8") - source("board.tcga/R/tcga_ui.R", encoding = "UTF-8") - source("board.upload/R/upload_module_batchcorrect.R", encoding = "UTF-8") - source("board.upload/R/upload_module_computepgx.R", encoding = "UTF-8") - source("board.upload/R/upload_module_initial_settings.R", encoding = "UTF-8") - source("board.upload/R/upload_module_makecontrast.R", encoding = "UTF-8") - source("board.upload/R/upload_module_normalization.R", encoding = "UTF-8") - source("board.upload/R/upload_module_outliers.R", encoding = "UTF-8") - source("board.upload/R/upload_module_preview_contrasts.R", encoding = "UTF-8") - source("board.upload/R/upload_module_preview_counts.R", encoding = "UTF-8") - source("board.upload/R/upload_module_preview_samples.R", encoding = "UTF-8") - source("board.upload/R/upload_plot_contraststats.R", encoding = "UTF-8") - source("board.upload/R/upload_plot_countstats.R", encoding = "UTF-8") - source("board.upload/R/upload_plot_pcaplot.R", encoding = "UTF-8") - source("board.upload/R/upload_plot_phenostats.R", encoding = "UTF-8") - source("board.upload/R/upload_server.R", encoding = "UTF-8") - source("board.upload/R/upload_ui.R", encoding = "UTF-8") - source("board.upload/R/upload_utils.R", encoding = "UTF-8") - source("board.user/R/appsettings_server.R", encoding = "UTF-8") - source("board.user/R/appsettings_ui.R", encoding = "UTF-8") - source("board.user/R/user_table_resources.R", encoding = "UTF-8") - source("board.user/R/userprofile_server.R", encoding = "UTF-8") - source("board.user/R/userprofile_ui.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_correlation_network.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_eigengene_clustering.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_enrichment.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_gclustering.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_gdendogram.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_heatmap_membership.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_membership_v_trait.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_module_graph.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_module_membership.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_MTrelationships.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_s_independence.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_plot_TOMheatmap.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_server.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_table_enrichment.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_table_genes.R", encoding = "UTF-8") - source("board.wgcna/R/wgcna_ui.R", encoding = "UTF-8") - source("board.wordcloud/R/wordcloud_plot_enrichment.R", encoding = "UTF-8") - source("board.wordcloud/R/wordcloud_plot_wordcloud.R", encoding = "UTF-8") - source("board.wordcloud/R/wordcloud_plot_wordtsne.R", encoding = "UTF-8") - source("board.wordcloud/R/wordcloud_server.R", encoding = "UTF-8") - source("board.wordcloud/R/wordcloud_table_enrichment.R", encoding = "UTF-8") - source("board.wordcloud/R/wordcloud_table_leading_edge.R", encoding = "UTF-8") - source("board.wordcloud/R/wordcloud_ui.R", encoding = "UTF-8") - source("modules/AuthenticationModule_functions.R", encoding = "UTF-8") - source("modules/AuthenticationModule_ui.R", encoding = "UTF-8") - source("modules/AuthenticationModule.R", encoding = "UTF-8") - source("modules/CookiesModule.R", encoding = "UTF-8") - source("modules/DatasetReport.R", encoding = "UTF-8") - source("modules/InfoModals.R", encoding = "UTF-8") - source("modules/InviteFriend.R", encoding = "UTF-8") - source("modules/NormalizeCountsModule.R", encoding = "UTF-8") - source("modules/PlotDownloadLogger.R", encoding = "UTF-8") - source("modules/QuestionModule.R", encoding = "UTF-8") - source("modules/TimerModule.R", encoding = "UTF-8") - source("modules/UserAccessControl.R", encoding = "UTF-8") - source("modules/UserInactivityControl.R", encoding = "UTF-8") - source("modules/UsersMapModule.R", encoding = "UTF-8") - source("modules/WelcomeBoard.R", encoding = "UTF-8") - source("ui/bs-components.R", encoding = "UTF-8") - source("ui/ui-alerts.R", encoding = "UTF-8") - source("ui/ui-bigdashplus.R", encoding = "UTF-8") - source("ui/ui-boardHeader.R", encoding = "UTF-8") - source("ui/ui-code.R", encoding = "UTF-8") - source("ui/ui-colors.R", encoding = "UTF-8") - source("ui/ui-defaults.R", encoding = "UTF-8") - source("ui/ui-DropDownMenu.R", encoding = "UTF-8") - source("ui/ui-fileInputArea.R", encoding = "UTF-8") - source("ui/ui-links.R", encoding = "UTF-8") - source("ui/ui-modalUI.R", encoding = "UTF-8") - source("ui/ui-PlotModule.R", encoding = "UTF-8") - source("ui/ui-startupModal.R", encoding = "UTF-8") - source("ui/ui-TableModule2.R", encoding = "UTF-8") - source("ui/ui-tooltip.R", encoding = "UTF-8") - source("ui/ui-utils.R", encoding = "UTF-8") - source("ui/ui-vizpanels.R", encoding = "UTF-8") - message("done! (sourcing all code)") + message('Note: sourcing all code...') + source('app/R/utils/auth.R',encoding='UTF-8') + source('app/R/utils/database.R',encoding='UTF-8') + source('app/R/utils/open_url.R',encoding='UTF-8') + source('app/R/utils/utils.R',encoding='UTF-8') + source('board.biomarker/R/biomarker_plot_boxplots.R',encoding='UTF-8') + source('board.biomarker/R/biomarker_plot_decisiontree.R',encoding='UTF-8') + source('board.biomarker/R/biomarker_plot_featurerank.R',encoding='UTF-8') + source('board.biomarker/R/biomarker_plot_heatmap.R',encoding='UTF-8') + source('board.biomarker/R/biomarker_plot_importance.R',encoding='UTF-8') + source('board.biomarker/R/biomarker_server.R',encoding='UTF-8') + source('board.biomarker/R/biomarker_ui.R',encoding='UTF-8') + source('board.clustering/R/clustering_plot_clustannot.R',encoding='UTF-8') + source('board.clustering/R/clustering_plot_clusterpca.R',encoding='UTF-8') + source('board.clustering/R/clustering_plot_genemodule.R',encoding='UTF-8') + source('board.clustering/R/clustering_plot_phenoplot.R',encoding='UTF-8') + source('board.clustering/R/clustering_plot_splitmap.R',encoding='UTF-8') + source('board.clustering/R/clustering_plot_table_parcoord.R',encoding='UTF-8') + source('board.clustering/R/clustering_server.R',encoding='UTF-8') + source('board.clustering/R/clustering_table_clustannot.R',encoding='UTF-8') + source('board.clustering/R/clustering_ui.R',encoding='UTF-8') + source('board.compare/R/compare_plot_compare1.R',encoding='UTF-8') + source('board.compare/R/compare_plot_compare2.R',encoding='UTF-8') + source('board.compare/R/compare_plot_cum_fc1.R',encoding='UTF-8') + source('board.compare/R/compare_plot_cum_fc2.R',encoding='UTF-8') + source('board.compare/R/compare_plot_expression.R',encoding='UTF-8') + source('board.compare/R/compare_plot_fcfc.R',encoding='UTF-8') + source('board.compare/R/compare_plot_genecorr.R',encoding='UTF-8') + source('board.compare/R/compare_server.R',encoding='UTF-8') + source('board.compare/R/compare_table_corr_score.R',encoding='UTF-8') + source('board.compare/R/compare_ui.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_plot_connectivityHeatmap.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_plot_connectivityMap.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_plot_cumEnrichmentPlot.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_plot_cumFCplot.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_plot_enrichmentGraph.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_plot_FCFCplots.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_plot_leadingEdgeGraph.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_plot_scatterPlot.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_server.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_table_foldchange.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_table_similarity_scores.R',encoding='UTF-8') + source('board.connectivity/R/connectivity_ui.R',encoding='UTF-8') + source('board.correlation/R/correlation_plot_barplot.R',encoding='UTF-8') + source('board.correlation/R/correlation_plot_cor_graph.R',encoding='UTF-8') + source('board.correlation/R/correlation_plot_correlation_UMAP.R',encoding='UTF-8') + source('board.correlation/R/correlation_plot_scattercorr.R',encoding='UTF-8') + source('board.correlation/R/correlation_server.R',encoding='UTF-8') + source('board.correlation/R/correlation_table_corr.R',encoding='UTF-8') + source('board.correlation/R/correlation_ui.R',encoding='UTF-8') + source('board.dataview/R/dataview_module_geneinfo.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_abundance.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_averagecounts.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_averagerank.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_boxplot.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_correlation.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_expression.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_genetypes.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_histogram.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_phenoassociation.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_phenoheatmap.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_tissue.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_totalcounts.R',encoding='UTF-8') + source('board.dataview/R/dataview_plot_tsneplot.R',encoding='UTF-8') + source('board.dataview/R/dataview_server.R',encoding='UTF-8') + source('board.dataview/R/dataview_table_contrasts.R',encoding='UTF-8') + source('board.dataview/R/dataview_table_rawdata.R',encoding='UTF-8') + source('board.dataview/R/dataview_table_samples.R',encoding='UTF-8') + source('board.dataview/R/dataview_ui.R',encoding='UTF-8') + source('board.drugconnectivity/R/drugconnectivity_plot_actmap.R',encoding='UTF-8') + source('board.drugconnectivity/R/drugconnectivity_plot_cmap_dsea.R',encoding='UTF-8') + source('board.drugconnectivity/R/drugconnectivity_plot_cmap_enplot.R',encoding='UTF-8') + source('board.drugconnectivity/R/drugconnectivity_plot_enplots.R',encoding='UTF-8') + source('board.drugconnectivity/R/drugconnectivity_plot_moa.R',encoding='UTF-8') + source('board.drugconnectivity/R/drugconnectivity_server.R',encoding='UTF-8') + source('board.drugconnectivity/R/drugconnectivity_table_cmap.R',encoding='UTF-8') + source('board.drugconnectivity/R/drugconnectivity_table_dsea.R',encoding='UTF-8') + source('board.drugconnectivity/R/drugconnectivity_ui.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_plot_barplot.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_plot_compare.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_plot_freq_top_gsets.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_plot_geneplot.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_plot_scatter.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_plot_top_enrich_gsets.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_plot_volcano.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_plot_volcanoall.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_plot_volcanomethods.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_server.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_table_enrichment_analysis.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_table_genes_in_geneset.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_table_gset_enrich_all_contrasts.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_table_n_sig_gsets.R',encoding='UTF-8') + source('board.enrichment/R/enrichment_ui.R',encoding='UTF-8') + source('board.expression/R/expression_plot_barplot.R',encoding='UTF-8') + source('board.expression/R/expression_plot_maplot.R',encoding='UTF-8') + source('board.expression/R/expression_plot_topfoldchange.R',encoding='UTF-8') + source('board.expression/R/expression_plot_topgenes.R',encoding='UTF-8') + source('board.expression/R/expression_plot_volcano.R',encoding='UTF-8') + source('board.expression/R/expression_plot_volcanoAll.R',encoding='UTF-8') + source('board.expression/R/expression_plot_volcanoMethods.R',encoding='UTF-8') + source('board.expression/R/expression_server.R',encoding='UTF-8') + source('board.expression/R/expression_table_fctable.R',encoding='UTF-8') + source('board.expression/R/expression_table_FDRtable.R',encoding='UTF-8') + source('board.expression/R/expression_table_genetable.R',encoding='UTF-8') + source('board.expression/R/expression_table_gsettable.R',encoding='UTF-8') + source('board.expression/R/expression_ui.R',encoding='UTF-8') + source('board.featuremap/R/featuremap_plot_gene_sig.R',encoding='UTF-8') + source('board.featuremap/R/featuremap_plot_gset_sig.R',encoding='UTF-8') + source('board.featuremap/R/featuremap_plot_table_gene_map.R',encoding='UTF-8') + source('board.featuremap/R/featuremap_plot_table_geneset_map.R',encoding='UTF-8') + source('board.featuremap/R/featuremap_server.R',encoding='UTF-8') + source('board.featuremap/R/featuremap_ui.R',encoding='UTF-8') + source('board.intersection/R/intersection_plot_contrast_correlation.R',encoding='UTF-8') + source('board.intersection/R/intersection_plot_foldchange_heatmap.R',encoding='UTF-8') + source('board.intersection/R/intersection_plot_scatterplot_pairs.R',encoding='UTF-8') + source('board.intersection/R/intersection_plot_table_venn_diagram.R',encoding='UTF-8') + source('board.intersection/R/intersection_server.R',encoding='UTF-8') + source('board.intersection/R/intersection_ui.R',encoding='UTF-8') + source('board.loading/R/loading_module_received.R',encoding='UTF-8') + source('board.loading/R/loading_module_shared.R',encoding='UTF-8') + source('board.loading/R/loading_server.R',encoding='UTF-8') + source('board.loading/R/loading_table_datasets_public.R',encoding='UTF-8') + source('board.loading/R/loading_table_datasets.R',encoding='UTF-8') + source('board.loading/R/loading_tsneplot.R',encoding='UTF-8') + source('board.loading/R/loading_ui.R',encoding='UTF-8') + source('board.loading/R/loading_utils.R',encoding='UTF-8') + source('board.pathway/R/pathway_enrichmap.R',encoding='UTF-8') + source('board.pathway/R/pathway_plot_enrichmap.R',encoding='UTF-8') + source('board.pathway/R/pathway_plot_go_actmap.R',encoding='UTF-8') + source('board.pathway/R/pathway_plot_go_network.R',encoding='UTF-8') + source('board.pathway/R/pathway_plot_reactome_actmap.R',encoding='UTF-8') + source('board.pathway/R/pathway_plot_reactome_graph.R',encoding='UTF-8') + source('board.pathway/R/pathway_plot_wikipathway_actmap.R',encoding='UTF-8') + source('board.pathway/R/pathway_plot_wikipathway_graph.R',encoding='UTF-8') + source('board.pathway/R/pathway_server.R',encoding='UTF-8') + source('board.pathway/R/pathway_table_go_table.R',encoding='UTF-8') + source('board.pathway/R/pathway_table_reactome.R',encoding='UTF-8') + source('board.pathway/R/pathway_table_wikipathway.R',encoding='UTF-8') + source('board.pathway/R/pathway_ui.R',encoding='UTF-8') + source('board.pathway/R/pathway_wikipathview.R',encoding='UTF-8') + source('board.pcsf/R/pcsf_plot_heatmap.R',encoding='UTF-8') + source('board.pcsf/R/pcsf_plot_network.R',encoding='UTF-8') + source('board.pcsf/R/pcsf_server.R',encoding='UTF-8') + source('board.pcsf/R/pcsf_table_centrality.R',encoding='UTF-8') + source('board.pcsf/R/pcsf_ui.R',encoding='UTF-8') + source('board.pcsf/R/util_pcsf.R',encoding='UTF-8') + source('board.signature/R/signature_plot_enplots.R',encoding='UTF-8') + source('board.signature/R/signature_plot_markers.R',encoding='UTF-8') + source('board.signature/R/signature_plot_overlap.R',encoding='UTF-8') + source('board.signature/R/signature_plot_volcano.R',encoding='UTF-8') + source('board.signature/R/signature_server.R',encoding='UTF-8') + source('board.signature/R/signature_table_enrich_by_contrasts.R',encoding='UTF-8') + source('board.signature/R/signature_table_genes_in_signature.R',encoding='UTF-8') + source('board.signature/R/signature_table_overlap.R',encoding='UTF-8') + source('board.signature/R/signature_ui.R',encoding='UTF-8') + source('board.singlecell/R/singlecell_plot_crosstabPlot.R',encoding='UTF-8') + source('board.singlecell/R/singlecell_plot_cytoplot.R',encoding='UTF-8') + source('board.singlecell/R/singlecell_plot_icpplot.R',encoding='UTF-8') + source('board.singlecell/R/singlecell_plot_mappingplot.R',encoding='UTF-8') + source('board.singlecell/R/singlecell_plot_markersplot.R',encoding='UTF-8') + source('board.singlecell/R/singlecell_plot_phenoplot.R',encoding='UTF-8') + source('board.singlecell/R/singlecell_server.R',encoding='UTF-8') + source('board.singlecell/R/singlecell_ui.R',encoding='UTF-8') + source('board.tcga/R/tcga_plot_survival.R',encoding='UTF-8') + source('board.tcga/R/tcga_server.R',encoding='UTF-8') + source('board.tcga/R/tcga_ui.R',encoding='UTF-8') + source('board.upload/R/upload_module_batchcorrect.R',encoding='UTF-8') + source('board.upload/R/upload_module_computepgx.R',encoding='UTF-8') + source('board.upload/R/upload_module_initial_settings.R',encoding='UTF-8') + source('board.upload/R/upload_module_makecontrast.R',encoding='UTF-8') + source('board.upload/R/upload_module_normalization.R',encoding='UTF-8') + source('board.upload/R/upload_module_outliers.R',encoding='UTF-8') + source('board.upload/R/upload_module_preview_contrasts.R',encoding='UTF-8') + source('board.upload/R/upload_module_preview_counts.R',encoding='UTF-8') + source('board.upload/R/upload_module_preview_samples.R',encoding='UTF-8') + source('board.upload/R/upload_plot_contraststats.R',encoding='UTF-8') + source('board.upload/R/upload_plot_countstats.R',encoding='UTF-8') + source('board.upload/R/upload_plot_pcaplot.R',encoding='UTF-8') + source('board.upload/R/upload_plot_phenostats.R',encoding='UTF-8') + source('board.upload/R/upload_server.R',encoding='UTF-8') + source('board.upload/R/upload_ui.R',encoding='UTF-8') + source('board.upload/R/upload_utils.R',encoding='UTF-8') + source('board.user/R/appsettings_server.R',encoding='UTF-8') + source('board.user/R/appsettings_ui.R',encoding='UTF-8') + source('board.user/R/user_table_resources.R',encoding='UTF-8') + source('board.user/R/userprofile_server.R',encoding='UTF-8') + source('board.user/R/userprofile_ui.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_correlation_network.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_eigengene_clustering.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_enrichment.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_gclustering.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_gdendogram.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_heatmap_membership.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_membership_v_trait.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_module_graph.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_module_membership.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_MTrelationships.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_s_independence.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_plot_TOMheatmap.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_server.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_table_enrichment.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_table_genes.R',encoding='UTF-8') + source('board.wgcna/R/wgcna_ui.R',encoding='UTF-8') + source('board.wordcloud/R/wordcloud_plot_enrichment.R',encoding='UTF-8') + source('board.wordcloud/R/wordcloud_plot_wordcloud.R',encoding='UTF-8') + source('board.wordcloud/R/wordcloud_plot_wordtsne.R',encoding='UTF-8') + source('board.wordcloud/R/wordcloud_server.R',encoding='UTF-8') + source('board.wordcloud/R/wordcloud_table_enrichment.R',encoding='UTF-8') + source('board.wordcloud/R/wordcloud_table_leading_edge.R',encoding='UTF-8') + source('board.wordcloud/R/wordcloud_ui.R',encoding='UTF-8') + source('modules/AuthenticationModule_functions.R',encoding='UTF-8') + source('modules/AuthenticationModule_ui.R',encoding='UTF-8') + source('modules/AuthenticationModule.R',encoding='UTF-8') + source('modules/CookiesModule.R',encoding='UTF-8') + source('modules/DatasetReport.R',encoding='UTF-8') + source('modules/InfoModals.R',encoding='UTF-8') + source('modules/InviteFriend.R',encoding='UTF-8') + source('modules/NormalizeCountsModule.R',encoding='UTF-8') + source('modules/PlotDownloadLogger.R',encoding='UTF-8') + source('modules/QuestionModule.R',encoding='UTF-8') + source('modules/TimerModule.R',encoding='UTF-8') + source('modules/UserAccessControl.R',encoding='UTF-8') + source('modules/UserInactivityControl.R',encoding='UTF-8') + source('modules/UsersMapModule.R',encoding='UTF-8') + source('modules/WelcomeBoard.R',encoding='UTF-8') + source('ui/bs-components.R',encoding='UTF-8') + source('ui/ui-alerts.R',encoding='UTF-8') + source('ui/ui-bigdashplus.R',encoding='UTF-8') + source('ui/ui-boardHeader.R',encoding='UTF-8') + source('ui/ui-code.R',encoding='UTF-8') + source('ui/ui-colors.R',encoding='UTF-8') + source('ui/ui-defaults.R',encoding='UTF-8') + source('ui/ui-DropDownMenu.R',encoding='UTF-8') + source('ui/ui-fileInputArea.R',encoding='UTF-8') + source('ui/ui-links.R',encoding='UTF-8') + source('ui/ui-modalUI.R',encoding='UTF-8') + source('ui/ui-PlotModule.R',encoding='UTF-8') + source('ui/ui-startupModal.R',encoding='UTF-8') + source('ui/ui-TableModule2.R',encoding='UTF-8') + source('ui/ui-tooltip.R',encoding='UTF-8') + source('ui/ui-utils.R',encoding='UTF-8') + source('ui/ui-vizpanels.R',encoding='UTF-8') + message('done! (sourcing all code)') } diff --git a/components/board.expression/R/expression_plot_volcano.R b/components/board.expression/R/expression_plot_volcano.R index 2d5ef078f..636abdaf0 100644 --- a/components/board.expression/R/expression_plot_volcano.R +++ b/components/board.expression/R/expression_plot_volcano.R @@ -79,6 +79,8 @@ expression_plot_volcano_server <- function(id, lfc <- as.numeric(lfc()) res <- res() + + symbols <- playbase::probe2symbol( probes = rownames(res), res, query = "symbol", fill_na = TRUE ) @@ -93,12 +95,16 @@ expression_plot_volcano_server <- function(id, ylab <- "Significance (-log10p)" } + names <- ifelse(is.na(res$gene_title), rownames(res), res$gene_title) + + return(list( x = x, y = y, ylab = ylab, symbols = symbols, features = rownames(res), + names = names, sel.genes = genes_selected()$sel.genes, lab.genes = genes_selected()$lab.genes, lab.cex = 1, @@ -115,6 +121,9 @@ expression_plot_volcano_server <- function(id, if (labeltype() == "symbol") { names <- pd[["features"]] label.names <- pd[["symbols"]] + } else if (labeltype() == "name") { + names <- pd[["symbols"]] + label.names <- pd[["names"]] } else { names <- pd[["symbols"]] label.names <- pd[["features"]] diff --git a/components/board.expression/R/expression_ui.R b/components/board.expression/R/expression_ui.R index 0844f9e3d..c7535908b 100644 --- a/components/board.expression/R/expression_ui.R +++ b/components/board.expression/R/expression_ui.R @@ -56,7 +56,7 @@ ExpressionInputs <- function(id) { placement = "top", options = list(container = "body") ), shiny::radioButtons(ns("labeltype"), "Plot labels:", - c("symbol", "probe"), + c("symbol", "probe", "name"), inline = TRUE ), withTooltip(