Sidebar Controls¶
The sidebar is always visible on the left side of the dashboard. It is organized from top to bottom as follows:
Username & Logout¶
At the very top of the sidebar, your username (e.g., "ejcha88") is displayed alongside a Logout button. Click Logout to end your session.
Project Selector¶
A dropdown labeled "Project" lets you switch between your saved analysis projects. Each project is identified by its name and NCBI accession ID (e.g., "[Sample] asd (PRJNA257197)").
Projects that are still being processed show a "- Not ready" label — these are waiting for the RNA-Seq pipeline to complete. You can select a ready project to load its analysis results into all visualization tabs.
Contrast Selector¶
When your project has multiple contrasts (i.e. multiple *.deseq2.results*.tsv files), a Contrast dropdown appears below the Project selector. It lets you switch which DESeq2 comparison is displayed across all visualization tabs. The contrast names are derived from the filenames (e.g., treatment_VS_control).
If only a single contrast file exists, this dropdown is hidden and that contrast is used automatically.
Filters¶
The Filters section provides threshold sliders and gene selection tools:
Adjusted p-value threshold¶
A slider ranging from 0.00 to 0.10 (default: 0.08). Genes with an adjusted p-value below this threshold are considered statistically significant. Lowering the value makes the filter more stringent; raising it includes more genes.
log2 Fold Change threshold¶
A slider ranging from 0.50 to 5.00 (default: 1.00). Genes must have an absolute log2 fold change above this value to be considered biologically meaningful. Increasing the value filters for larger expression changes.
Info
These two thresholds work together to define "significant" genes displayed in the Volcano plot, Bar chart, and other views.
Top N¶
A slider ranging from 5 to 50 (default: 20). Controls how many top items are displayed in enrichment charts (GO and KEGG tabs) and other ranked visualizations.
Filter by gene ID¶
A searchable dropdown that lets you narrow the displayed data to specific gene identifiers. Click the dropdown and begin typing a gene ID to search, or browse the list. You can select multiple genes. When genes are selected here, only those genes will appear in the plots and tables.
Filter by gene desc¶
Similar to the gene ID filter, but searches and filters by the gene's functional description text. Useful when you know the function or pathway you are interested in but not the specific gene ID.
Highlight gene ID¶
A searchable dropdown that lets you visually highlight specific genes on the plots (e.g., on the Volcano plot). Unlike the filter options, highlighting does not remove other genes — it simply draws attention to your genes of interest using the "Selected" highlight color.
Highlight genes desc¶
Same as Highlight Gene ID, but matches genes by their description text.
PCA Axes¶
These controls determine which principal components are displayed on the PCA tab:
- X axis — Dropdown to select the principal component for the horizontal axis (default: PC1).
- Y axis — Dropdown to select the principal component for the vertical axis (default: PC2).
You can change these to explore other component combinations (e.g., PC1 vs PC3).
Appearance (Collapsible Section)¶
The Appearance section is a collapsible panel (click the header or chevron to expand/collapse). It contains all visual customization controls:
Dot Size¶
A slider ranging from 5.00 to 14.00 (default: 6.00). Controls the size of data points on scatter plots such as the PCA Score Plot and Volcano Plot.
Plot Height¶
Ranges from 300 to 1200 pixels (default: 500). Controls the height of generated plots across all report tabs. Some reports (e.g., Enrichment Compare, Venn) may scale up beyond this value when content requires more space, but will never shrink below it.
Plot Width¶
Ranges from 400 to 1600 pixels (default: 800). Controls the width of generated plots across all report tabs. Some reports (e.g., Heatmap by Sample, Co-expression correlation matrix) may scale up beyond this value when there are many samples or genes, but will never shrink below it.
Colors¶
Color pickers for customizing plot elements:
| Color | Purpose | Default |
|---|---|---|
| Up | Upregulated genes | Red |
| Down | Downregulated genes | Blue |
| Select | Highlighted/selected genes | Orange |
| Others | Non-significant or other genes | Grey |
| Title | Plot titles | Black |
| BG | Background color of the plot area | Dark grey |
| Axis | Axis labels and tick marks | Dark grey |
Click any color swatch to open a color picker and choose a custom color.
Font¶
- Font size — A slider ranging from 8 to 24 (default: 12). Controls the base font size for plot labels, axis text, and titles.
- Font color — A color picker for the main font color used in plots (default: black).
Threshold Lines¶
- Line type — A dropdown to choose the line style: dash (default), solid, dot, or other options.
- Line color — A color picker for the threshold line color (default: grey).
Presets¶
Four preset buttons are arranged in a 2x2 grid at the bottom of the Appearance section:
| Preset | Font Size | Dot Size | Plot Size | Best for |
|---|---|---|---|---|
| Publication | 14 | 8 | 600 x 900 | Journal figures |
| Presentation | 18 | 10 | 700 x 1200 | Slides and talks |
| Screen | 12 | 6 | 500 x 800 | On-screen exploration |
| Reset | — | — | — | Restores all settings to defaults |
Clicking a preset instantly applies its values. The Reset button clears all customizations and restores both appearance and filter settings to their original default values.
New Project¶
At the very bottom of the sidebar, a "New Project" button opens the project creation workflow. See Projects for details.