Documentation of significance-analysis.md (#253)

* Documentation of significance-analysis.md

* Update comparisons.

docs/interface-details/significance-analysis.md

@@ -3,4 +3,74 @@ title: "Significance Analysis"
 layout: default
 parent: Interface Details
 nav_order: 4
----
+---
+
+# Significance Analysis
+
+The Significance Analysis tab is divided into two main sections: the side panel and the main panel.
+
+## Side Panel
+
+In the side panel, you have the following options:
+
+- **Choose groups to compare**: This allows you to select the groups you want to compare.
+- **Select your desired comparisons**: Here you input the specific comparisons you 
+  want to make. You enter the groups in the format `Treatment:Control`. Multiple 
+  comparison pairs can be entered at once.
+- **Test method**: You can select the statistical test method to use. You can choose 
+  between [T-test](https://en.wikipedia.org/wiki/Student%27s_t-test), [Wilcoxon Rank 
+  Sum Test]((https://en.wikipedia.org/wiki/Mann–Whitney_U_test), and [Welch's T-test](https://en.wikipedia.org/wiki/Welch%27s_t-test). 
+  If you used `vst_DESeq` as the [preprocessing method](pre-processing.md), DESeq2 
+  will use the [Wald test](https://en.wikipedia.org/wiki/Wald_test).
+
+- **Significance level**: This slider allows you to set the significance level for the analysis, ranging from 0.005 to 0.1.
+
+- **Test correction**: You can choose the method for multiple testing correction.
+
+- **Get Significance Analysis**: Clicking this button will perform the significance analysis based on the selected parameters.
+
+## Main Panel
+
+The main panel displays the results of the significance analysis. The main panel has several tabs:
+- **Result Visualization**: This tab shows similarities and differences between the groups you compared.
+  - **Visualization Choices**: Allows you to customize the visualization of the results.
+    - **Select your desired comparisons to visualize**: Choose which comparisons to include in the visualization.
+    - **Visualization method**: Select the type of plot to use. If the number of comparisons is 
+      smaller than 4, you can choose between UpSetR plot and Venn diagram. If the 
+      number of comparisons is larger than 4, only the UpSetR plot is available.
+    - **Type of significance to look at**: Choose between Significant and Significant 
+      unadjusted.
+    - **Intersections to highlight**: Specify the number of intersections to 
+      highlight in the plot. (Only available for UpSetR plot)
+  - **Venn Diagram**: Shows the intersections of significant results across 
+    different comparisons as overlapping circles. The number within each 
+    intersection is equal to the number of significant results that the circles 
+    sharing the intersection have in common.
+  - **UpSetR Plot**: The UpSetR plot section visualizes the intersections of significant results across different comparisons.
+    - **Intersection Size**: The bars represent the number of significant results for each intersection.
+    - **Set Size**: The horizontal bars show the number of significant results in each comparison group.
+    - **Intersections**: The dots and lines indicate which groups are part of each intersection.
+  - **Download Options**: You can save the plots in different file formats such as 
+    PNG, TIFF, and PDF. You also have the option to download the underlying R code 
+    and data. For more information, check out [Interface 
+      Details](interface-details.md).
+- **Comparison tabs**: For each selected comparison, a separate tab is created in 
+  which the results can be viewed. They consist of a Volcano plot and a table.
+  - **Table**: A sortable table, displaying pvalue, padj, log2FoldChange, and other 
+    information for each entity tested. The table can be downloaded as a `.csv` or `.
+    xlsx` file. The table can be sorted by clicking on the column headers.
+  - **Volcano Plot**: The volcano plot section is divided into two plots:
+    - **Corrected p-Values**: Shows the log fold change versus the corrected p-values.
+    - **Uncorrected p-Values**: Shows the log fold change versus the uncorrected p-values.
+    - Both plots simultaneously or separately can be downloaded directly in common 
+      formats (e.g., PNG, TIFF, PDF) or sent to the report. You can also download 
+      the underlying R code and data. For more information, check out [Interface 
+      Details](interface-details.md).
+
+### Other Notes
+
+- **Question Marks**: The displayed question marks provide quick and immediate help. However, since you are reading this documentation, you found the extensive version. Hope it helped!
+- **Interpretation**: The plots and table can give insights into the significant 
+  changes between the compared groups. Adjusting the significance level and thresholds 
+  can help in identifying the most relevant results. Checking the intersections can 
+  point towards commonalities between the groups.