--- a +++ b/src/dash/app.py @@ -0,0 +1,80 @@ +import dash + +import dash_bootstrap_components as dbc +external_stylesheets=[dbc.themes.BOOTSTRAP] + +# add GA script +external_scripts = [ + {'src':'/assets/gtag.js'}, +] + +app = dash.Dash(__name__, + suppress_callback_exceptions=True, + external_stylesheets=external_stylesheets, + external_scripts=external_scripts) + +app.title = 'COVID-19 Multi-Omics' + +server = app.server + +### load shared data ### +from data import get_omics_data, get_biomolecule_names +import datetime + +print() +print(datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")) +print("Loading data for app...") +print() +# load metabolomics data matrix +print("Loading metabolomics data...") +metabolomics_df, metabolomics_quant_range = get_omics_data(dataset='metabolomics', with_metadata=True) +print("Metabolomics data shape: {}".format(metabolomics_df.shape)) +print("Loading lipidomics data...") +lipidomics_df, lipidomics_quant_range = get_omics_data(dataset='lipidomics', with_metadata=True) +print("Lipidomics data shape: {}".format(lipidomics_df.shape)) +print("Loading proteomics data...") +proteomics_df, proteomics_quant_range = get_omics_data(dataset='proteomics', with_metadata=True) +print("Proteomics data shape: {}".format(proteomics_df.shape)) +print("Loading transcriptomics data...") +transcriptomics_df, transcriptomics_quant_range = get_omics_data(dataset='transcriptomics', with_metadata=True) +print("Transcriptomics data shape: {}".format(transcriptomics_df.shape)) + +# make biomolecule_name_dict +metabolomics_biomolecule_names_dict = get_biomolecule_names(dataset='metabolomics') +lipidomics_biomolecule_names_dict = get_biomolecule_names(dataset='lipidomics') +proteomics_biomolecule_names_dict = get_biomolecule_names(dataset='proteomics') +transcriptomics_biomolecule_names_dict = get_biomolecule_names(dataset='transcriptomics') + +# define dataset dictionaries +dataset_dict = { + "Proteins":"proteomics", + "Lipids":"lipidomics", + "Metabolites":"metabolomics", + "Transcripts":"transcriptomics", + "Combined Biomolecules":"combined" + } + +df_dict = { + "proteomics":proteomics_df, + "lipidomics":lipidomics_df, + "metabolomics":metabolomics_df, + "transcriptomics":transcriptomics_df +} + +quant_value_range_dict = { + "proteomics":proteomics_quant_range, + "lipidomics":lipidomics_quant_range, + "metabolomics":metabolomics_quant_range, + "transcriptomics":transcriptomics_quant_range +} + +global_names_dict = { + "proteomics":proteomics_biomolecule_names_dict, + "lipidomics":lipidomics_biomolecule_names_dict, + "metabolomics":metabolomics_biomolecule_names_dict, + "transcriptomics":transcriptomics_biomolecule_names_dict, + "combined":{**proteomics_biomolecule_names_dict, + **lipidomics_biomolecule_names_dict, + **metabolomics_biomolecule_names_dict, + **transcriptomics_biomolecule_names_dict} +}