From dd8c50df373ba1609f9c9588d10b8dca1df5dac9 Mon Sep 17 00:00:00 2001 From: Paul Jonas Jost <70631928+PaulJonasJost@users.noreply.github.com> Date: Tue, 9 Jul 2024 16:42:00 +0200 Subject: [PATCH] Documentation of significance-analysis.md (#253) * Documentation of significance-analysis.md * Update comparisons. --- .../significance-analysis.md | 72 ++++++++++++++++++- 1 file changed, 71 insertions(+), 1 deletion(-) diff --git a/docs/interface-details/significance-analysis.md b/docs/interface-details/significance-analysis.md index 4509828b..8f5f6afe 100644 --- a/docs/interface-details/significance-analysis.md +++ b/docs/interface-details/significance-analysis.md @@ -3,4 +3,74 @@ title: "Significance Analysis" layout: default parent: Interface Details nav_order: 4 ---- \ No newline at end of file +--- + +# 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.