Main plot
This card contains an interactive volcano or MA plot, where each dot represents one feature. Black dots highlight statistically significant DE features.
Plot settings
Adjust your preferences by clicking the gear icon:
- Choose the plot type (volcano of MA)
- Set false discovery rate (FDR) threshold for significance
- Set absolute log fold change (|logFC|) threshold for significance
Selections
- Hover the cursor over a dot to select that feature
- Draw a rectangle to select multiple features
Each selection will activate related elements in other panels. Specifically, the feature plot and information table will display data about the selected feature(s); the enrichment panel will show the statistically enriched functional terms.
Feature plot
This card displays the expression or abundance levels of selected features (genes or proteins). For a single feature, it presents an intensity versus group plot. When multiple features are selected, it shows a heatmap of features against samples or groups.
Plot settings
Adjust your preferences by clicking the gear icon:
- ‘X-axis variable’ - variable name (column name in the
metdatadata frame) to use on the X axis - ‘Colour variable’ - variable name (column name in the
metdatadata frame) to set colour to points - ‘Heatmap normalised per row’ - if enabled, each row (gene) is normalised to its own mean; if unselected, the original expression or abundance data are shown
- ‘Intensity scale’ - Choose between a linear or logarithmic scale. If logarithmic scale is chosen, any non-positive values will be removed before plotting.
Feature information
This card provides details about features (genes or proteins) selected from the volcano or MA plot. Information displayed includes the name (gene symbol), description, log fold change, and false discovery rate.
Interaction
- You can sort the data in the table by any column. Simply click the small triangles at the top of each column to reorder the entries.
- Click on any row to select it; this will activate related elements of the application. Specifically, the feature plot will display the selected feature, and the volcano/MA plot will highlight the feature’s location.
Functional enrichment
This card displays a table of statistically significant terms, calculated instantly when multiple features (genes or proteins) are selected from the volcano or MA plot. The terms are presented in order of their odds ratio (OR). Each entry in the table provides the term ID, a description, the number of selected features annotated with this term, the odds ratio, and a list of the feature names included.
Settings
Adjust your preferences by clicking the gear icon:
- Select the ontology to be displayed (GO, Reactome, KEGG)
- Set the threshold for false discovery rate to define significant terms
Interaction
- Sort data within the table by clicking the small triangles at the top of each column.
- Click on any row to select it; this will activate related elements of the application. The feature information table and both plots will then highlight the features associated with the selected term.