Documentation of Data Selection (#269)

* Data selection Documentation

docs/interface-details/selection.md

@@ -6,3 +6,97 @@ nav_order: 1
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 # 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.