View Source

The volcano plot is a special 2-D scatter plot used to visualize significance and the magnitude of changes in features (e.g. genes or transcripts) within a given comparison. By convention, the X-axis represents the fold change between the two groups and is on a log₂ scale. On the other hand, the Y-axis shows negative log10 of the p-values from the statistical test of the comparison.

As a prerequisite for invoking the volcano plot, you must run a Differential gene expression analysis. When setting-up the analysis, include all relevant contrasts you would like to view the volcano plots for.

Once the analysis is complete, open the resulting Feature list data node. Navigate to the Gene list section of the page and click on the volcano plot icon, located on the left of the table header (Figure 1).

Flow Documentation > Volcano Plot > invoke volcano plot.png

Each point on the plot represents the statistical result for a single feature (e.g. gene, transcript etc.). The black vertical and horizontal lines represent threshold of fold change and p-value respectively. By default the two vertical lines represent fold changes of -2 and +2, the horizontal line represents significant p-value of 0.05. Features that are up/down-regulated by at least 2 fold and have a p-value less than 0.05 are at the upper-right and upper-left corner of the plot, they are highlighted in different colors. By default, significantly up-regulated features are in red, significantly down-regulated features are in blue, and the remaining features are in grey or black (Figure 2). The plot header is derived from the name of the contrast.

Flow Documentation > Volcano Plot > volcano plot.png

The Axes and Statistics menus allow to customize which data sources will be used for the axes as well as annotations, limits and significance thresholds for the plot (Figure 3).

Flow Documentation > Volcano Plot > volcano plot axes and statistics card.png

The colors can also be customised using the Style menu (Figure 4).

Flow Documentation > Volcano Plot > volcano plot style card.png

Flow Documentation > Volcano Plot > volcano plot change color.png

You can also highlight and label any of the genes in the plot (Figure 5).

Flow Documentation > Volcano Plot > volcano plot highlight a gene.png

ghjkl

Click the Export image button on the left panel to save a PNG, SVG, or PDF image to your computer.

Click the To notebook button on the left panel to send the image to a page in the Notebook.

ghjkl