5  Volcano plot

Volcano plot is a nice tool to visualize in a two-dimensional way for differentially methylated CpG site or differentially expressed genes using the statistical p-values as well as the fold change value. Like a volcano, the plot can show the significant or insignificant data in a scatter plot manner. Here with methylR, we used plotly output to visualize the volcano plot to see the CpG or gene name (if the data from the differential analysis) with their respective p-values (adjusted p-values) and the logFC (or mean methylation difference).

5.1 How to use

5.1.1 Data upload & Parameters setup

5.1.1.1 Data upload

  1. User needs to upload a Tab (.txt) file with adjusted p-values and logFC values. At present, user can use the DMCs data file directly generated from the main analysis (see Chapter 1).
  2. To setup the adjusted p-value, user can change the cut-off. Default is setup to 0.01.
  3. LogFC cut-off can also be changed as per user requirement. Default is setup to 0.3.
  4. After the file upload and setting up the cut-off for adjusted p-value and logFC, click the “Run Analysis” button.

5.2 Analysis result

5.2.1 Volcano plot

  1. The figure will generated as soon as the computation finishes. However, it might takes some more time depending on the size of the file. If user upload a file with 750K rows, it will take 3-5 minutes to generate the figure (See Appendix D). It is noteworthy that this big data in volcano plot, may be unstable in the browser.
  2. User can download the plot as figure (same as before) and the dynamic figure as a html file.
Note

Please note displaying of the volcano plot will take some time, even after the warning “generating plot, please wait…” disappears. Please wait for 1-2 minutes to get the visualization. The same may happen to the volcano plot data table.

Volcano plot
Tip

Volcano plot figure colors annotation- Significant & Fold Change, Significant , FoldChange or NotSignificant

  1. On the right tab, user can also see the volcano data table which is useful when they are using the full dataset from the main analysis result (See Chapter 1).

5.2.2 Volcano data

One data table will be generated using the input data and will have a column marked with Significant & Fold Change, Significant , FoldChange or NotSignificant depends on the adjusted p-value and logFC cut-off.

Volcano data table

5.3 R packages used

  1. plotly

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