Volcano plot - stjude/proteinpaint GitHub Wiki

The volcano plot visualizes differential analysis results by plotting statistical significance (-log₁₀(p-value)) against fold change (log₂(fc)).

The colors represent the selected control and case group colors as defined in the Groups tab of the portal UI. If no selections were made, both groups default to red.

Data points with zero p-values are plotted at the lowest nonzero p-value in the plot data.

Follow the instructions from the differential analysis app wiki page.

Users can highlight genes, add confounders, launch the box plot, etc. using the action buttons, p value table, and configure the display from the burger menu to the left of the plot.

Hovering over the rows in the p value highlights the data point in the plot. Clicking on the row allows the highlight to persist.

Clicking on the data point opens the data in both groups. If using gene expression data for example, clicking on the gene will display that gene in each group.

The buttons above the default plot display the images and statistics as well as show/hide the p value table to the left.

For gene expression, two additional buttons appear: Confounding factors and Genes.

• Confounding factors: Add confounding factors by selecting a term from menu and click submit. The plot will rerender with data accounting for the confounding factors. Note, the button is not available when the selected method is Wilcoxon or when there are great than 100 total samples and edgR is the selected method.
• Genes: Highlight genes in the volcano plot by inputing in the search bar or use a list from pre-defined datasets. Create a gene list from the UI and click submit to see the data points highlighted in the volcano. If a gene selected is not available, the display will show the gene with a line through. The Cancel highlight button in the top right removes the highlight.

Click on the burger menu in the upper lefthand side to see the controls. The default plot allows users to change the colors, size, fold change, and p-value type (i.e. original or adjusted).

For gene expression, additional controls to change the method, minimum read count, and total read count are available in the burger menu.