Circomics.md
In bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

Show multi-Omics Data in Circular Layout

The world Circomics comes from the association between Circos and Omics.

Circos is a package for visualizing data and information with circular layouts. User can visualize multiple matrices of Omics data at the same time and makes easy the exploring of relationships between dimensions using coloring sectors.

This function uses CoffeeWheel package developped by Dr. Arman Aksoy.

Studies in Wheel

User needs to: Choice in which Studies is interested. Visualize the availability of dimensions by checking Availability. + The output is a table with Yes/No availability. * Load Omics data for selected Studies by checking Load. The output is a list of loaded dimensions for selected Studies.

When Profiles Data are loaded, the button Load Profiles in Datasets appears. It uploads all Profiles Data to Processing panel for more exploring or analysis.

Availability

Availability checkbox checks existing genetic profiles for each selected study. Tis function displays result in table.

Availibility

(Push) Load Profiles data in Datasets (to Processing Panel)

For every dimension, the tables are merged by study and saved as: xCNA, xMetHM27, xMetHM450, xmiRNA, xmRNA, xMut, xRPPA in Datasets (Processing panel).

Pull User Data in circular Layout

Comparing experimental analysis to existing cancer genomics data could be used to predict the risk of cancer disorder using epigenmics profiles. User can import its experimental data from Processing panel and pull them to circular layout. In the following case, we pulled xCNA and xMut (User data) dataframes to circular layout with luad_tcga_pub and blca_tcga_pub studies. User can remove and pull him data for all existing dimension. Legend checkbox displays the meaning of the color palette.

Mutation Frequency of two cancers studies compared to User Data

Format of user data

Mutation: A data frame with at less two column named gene_symbol and mutation. All other dimensions: A data frame with: first column named id. that has the study/cancer reference the remain columns named by the gene symbol and have the value of the dimension for each study.