Comut-viz is an online tool to generate comutation plot, which delivers a global view of the mutation landascape of large-scale genomic studies. It accpets a table of mutation data as input, interactively filters it and visualize the top mutated genes in a customizable comutation plot.

Three input files are submitted on this page:

Mutation Data File: This file is required. It should be a table of mutation data, commonly a MAF file. It could also be a tab/comma delimited text file with a .txt, .csv or .tsv extension. The file should have a header and at least three columns representing sample ID, gene symbol and mutation type. The column names in the header are flexible. (example 1, example 2)

Sample Metadata File: This file is optional. It should be a tab/comma delimited text file with a .txt, .csv or .tsv extension. It must have a header and a sample ID column containing the same sample IDs as in the mutation data file. The sample ID column names do not need to be the same (example 1).

Since v0.8.2, users can visualize sample metadata as bar plots. Please check the news page for more details.

The app by default ignores comment lines starting with "#" in the above input files. Users can disable this behavior by unchecking the checkbox above before any file submission. If there are comment lines in other formats, please delete them before submitting to the app.

Gene Groups File: This file is optional. It should be a yaml file with a .yml extension. The file configures how genes are grouped in the plot. An example file is provided here. A gene can belong to multiple gene groups in the file. A special "__order" key can be specified in the file to determine the order of the gene groups shown in the plot. If the gene groups file is provided, the app will only show the overlapping genes between this file and the mutation data file. You can test this feature by first submitting the example gene groups file and then click on the example 141k button.

Example Buttons: Users can test the app using the two example buttons. One loads a mutationa data file with 5k rows and its metadata, and the other loads a large mutation data file with 141k rows.