configuration.yaml

module_files:
  - "modules/dashboardmodule.R"
  - "modules/cellcontentmodule.R"
  - "modules/immuneinterfacemodule.R"
  - "modules/groupsoverviewmodule.R"
  - "modules/survivalmodule.R"
  - "modules/immunomodulatormodule.R"
  - "modules/tilmodule.R"
  - "modules/immunefeaturesmodule.R"
  - "modules/iotargetmodule.R"
  - "modules/datainfomodule.R"
  - "modules/drivermodule.R"
  - "modules/subtypeclassifiermodule.R"
  - "modules/submodules.R"
  - "modules/distribution_plot_module.R"
  - "modules/cytokinenetwork.R"
  - "modules/cellimagemodule.R"
  - "modules/cnvmodule.R"
  - "modules/germlinemodule.R"
  - "modules/germlineheritability.R"
  - "modules/germlinegwas.R"
  - "modules/germlinerarevariants.R"
  - "modules/ioresponseoverviewmodule.R"
  - "modules/ioresponsesurvivalmodule.R"
  - "modules/ioresponse_distribution_module.R"
  - "modules/ioresponseimmunomodulatormodule.R"
  - "modules/ioresponsefeaturesmodule.R"
  - "modules/ioresponsemultivariate.R"
  
function_files:
  - "functions/load_data.R"
  - "functions/transform.R"
  - "functions/drilldown.R"
  - "functions/utils.R"
  - "functions/boxplot.R"
  - "functions/heatmap.R"
  - "functions/kmplot.R"
  - "functions/histogram.R"
  - "functions/format.R"
  - "functions/scatterplot.R"
  - "functions/violinplot.R"
  - "functions/mosaicplot.R"
  - "functions/barplot.R"
  - "functions/forestplot.R"
  - "functions/manhattanplot.R"
  - "functions/subtype_classifier.R"
  - "functions/tablef_fun.R"
  - "functions/imageplot.R"
  - "functions/event_data_utils.R"
  - "functions/extracellnet_utils.R"
  - "functions/cellimage_utils.R"
  - "functions/iomodules_utils.R"
  - "functions/germline_utils.R"

page_files:
  - "pages/aboutpage.R"
  - "pages/explorepage.R"
  - "pages/toolspage.R"
  - "pages/docspage.R"
  - "pages/resourcespage.R"

libraries:
  - "shinydashboard"
  - "plotly"


bq_remote: false # set data as remote (BigQuery) or local (on disk)
gs_remote: false
  
cell_content_local:
  - "Lymphocytes.Aggregate1"
  - "T.cells.CD8"
  - "T_cells_CD4.Aggregate2"
  - "Macrophage.Aggregate1"

cell_content_bq:
  - "Lymphocytes.Aggregate1"
  - "T_cells_CD8"
  - "T_cells_CD4_Aggregate2"
  - "Macrophage_Aggregate1"
 
diversity_metric_choices:
  - "Evenness"
  - "Shannon"
  - "Richness"

receptor_type_choices:
  - "TCR"
  - "BCR"
  
immunomodulator_groups:
  - "Gene_Family"
  - "Super_Category"
  - "Immune_Checkpoint"
  - "Function"
  
immunotarget_groups:
  - "Therapy Type"
  - "Pathway"

immune_groups:
  - "Subtype_Immune_Model_Based"
  - "Study"
  - "Subtype_Curated_Malta_Noushmehr_et_al"
  
cell_type_aggregates:
  - "Immune Cell Proportion - Original"
  - "Immune Cell Proportion - Multipotent Progenitor Cell Derivative Class"
  - "Immune Cell Proportion - Common Lymphoid and Myeloid Cell Derivative Class"
  - "Immune Cell Proportion - Differentiated Lymphoid and Myeloid Cell Derivative Class"

correlation_methods:
  - "Spearman": "spearman" 
  - "Pearson": "pearson"
  - "Kendall": "kendall"