diff --git a/docs/interface-details/selection.md b/docs/interface-details/selection.md index 24b41bad..938f6df0 100644 --- a/docs/interface-details/selection.md +++ b/docs/interface-details/selection.md @@ -6,3 +6,97 @@ nav_order: 1 --- # Data Selection + +The Data Selection tab is the initial step to upload and manage your data in cOmicsART. This section is divided into two main areas: the side panel and the main panel. + +## Side Panel + +The side panel offers several tabs for different data input methods. The data Upload +and possibile strctures are dtailed in the [Data Input](required-data-input.md). +Nonetheless, here is a short overview: + +### File Input + +- **Omic Type that is uploaded**: Select the type of omics data you are uploading (Transcriptomics, Lipidomics, Metabolomics). + +- **Upload data matrix**: Upload your data matrix file. Rows should be entities (e.g., genes) and columns should be samples. + +- **Upload sample annotation**: Upload the sample annotation file. Rows should be samples. + +- **Upload entities annotation matrix**: Upload the entities annotation matrix file. + +- **Inspect data**: Click this button to inspect the uploaded data. This will open a + Modal, in which you can see how the application interprets your data, whether it is + able to differentiate between the different columns and - through additional tests - + whether the data as you uploaded it is deemed good to go. + +- **Upload new data**: Click this button to upload new data files. + +### Precompiled + +- **Omic Type that is uploaded**: Select the type of omics data you are uploading (Transcriptomics, Lipidomics, Metabolomics). + +- **Load precompiled data**: Upload a precompiled data file (e.g., RDS file). It has + the benefit, that - once saved - you only need to upload a single file now instead + of all three. + +- **Upload new data**: Click this button to upload new precompiled data files. + +### Metadata + +Very similar to the `File Input`, but replacing the sample annotation with the +[Metadatasheet](https://www.nature.com/articles/s41597-024-03349-2). + +- **Omic Type that is uploaded**: Select the type of omics data you are uploading (Transcriptomics, Lipidomics, Metabolomics). + +- **Upload data matrix**: Upload your data matrix file. Rows should be entities (e.g., genes) and columns should be samples. + +- **Upload your Meta Data Sheet**: Upload your metadata sheet. This currently replaces the sample annotation. + +- **Upload entities annotation matrix**: Upload the entities annotation matrix file. Rows should be entities. + +- **Upload new data**: Click this button to upload new metadata files. + +### Testdata + +- **Omic Type that is uploaded**: Select the type of omics data you are uploading (Transcriptomics, Lipidomics, Metabolomics). + +- **Start straight away with a test-dataset!**: Click this button to start with a test dataset. + +## Main Panel + +The main panel provides options for detailed data selection: + +- **Adding Gene Annotation**: In case of transcriptomics data, you can add gene + annotation to your sample. For this you only need to choose **Which Organism?** and + click the **Add Gene Annotation** button. + +### Row Selection - Biochemical Entities + +- **Which annotation type do you want to select on?**: Here you select a column of + your entitie annotation. Based on this column you can then select specific rows to + include through **Which entities to use?**. This might be either entitie names or + depending on the column you select also functional groups like e.g. "All Protein + Coding Genes". The more information you have on your entities, the better you can + select here. + +### Sample Selection + +- **Which annotation type do you want to select on?**: Similar to the row selection you select a column of + your sample annotation. Based on this column you can then select specific samples to + include through **Which entities to use?**. You can e.g. select specific + samples or all samples from a specific experiment. Again, the more information you + have on the samples, the better you can choose here. + +### Save Input As RDS + +- **Save file input to upload later**: Click this button to save the file input as an RDS file for later use. + +### Start the Journey + +- **Start the Journey**: Click this button to proceed with the analysis. This will + automatically bring you to the [Pre-processing tab](pre-processing.md). + +### Other Notes + +- **Question Marks**: The displayed question marks provide quick and immediate help. They offer guidance and additional information about the options available.