What it does

This tool creates a Volcano plot using ggplot2. Points can be labelled via ggrepel. It was inspired by this Getting Genetics Done blog post.

In statistics, a Volcano plot is a type of scatter-plot that is used to quickly identify changes in large data sets composed of replicate data. It plots significance versus fold-change on the y and x axes, respectively. These plots are increasingly common in omic experiments such as genomics, proteomics, and metabolomics where one often has a list of many thousands of replicate data points between two conditions and one wishes to quickly identify the most meaningful changes. A volcano plot combines a measure of statistical significance from a statistical test (e.g., a p value from an ANOVA model) with the magnitude of the change, enabling quick visual identification of those data-points (genes, etc.) that display large magnitude changes that are also statistically significant.

A volcano plot is constructed by plotting the negative log of the p value on the y axis (usually base 10). This results in data points with low p values (highly significant) appearing toward the top of the plot. The x axis is the log of the fold change between the two conditions. The log of the fold change is used so that changes in both directions appear equidistant from the center. Plotting points in this way results in two regions of interest in the plot: those points that are found toward the top of the plot that are far to either the left- or right-hand sides. These represent values that display large magnitude fold changes (hence being left or right of center) as well as high statistical significance (hence being toward the top).

Source: Wikipedia

Inputs

A tabular file containing the columns below (additional columns may be present):

• P value
• FDR / adjusted P value
• Log fold change
• Labels (e.g. Gene symbols or IDs)

All significant points, those meeting the specified FDR and Log Fold Change thresholds, will be coloured, red for upregulated, blue for downregulated. Users can choose to apply labels to the points (such as gene symbols) from the Labels column. To label all significant points, select "Significant" for the Points to label option, or to only label the top most significant specify a number under "Only label top most significant". Users can label any points of interest through selecting Points to label "Input from file" and providing a tabular labels file. The labels file must contain a header row and have the labels in the first column. These labels must match the labels in the main input file.

Outputs

A PDF containing a Volcano plot like below. The R code can be output through Output Options in the tool form.