inst/app/tools/help/pivotr.md

In kmezhoud/bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

Create pivot tables to explore your data

If you have used pivot-tables in Excel the functionality provided in the Pivot tab should be familiar to you. Similar to the Explore tab, you can generate summary statistics for variables in your data. You can also easily generate frequency tables. Perhaps the most powerful feature in Pivot is that you can describe the data by one or more other variables.

For example, with the epiGenomics data select Genes, Diseases and CNA from the Categorical variables drop-down. You can drag-and-drop the selected variables to change their order. The categories for the first variable will be the column headers. After selecting these three variables a frequency table of data with different Diseases and Genes. Choose Row, Column, or Total from the Normalize drop-down to normalize the frequencies by row, column, or overall total. If a normalize option is selected it can be convenient to check the Percentage box to express the numbers as percentages. Choose Color bar or Heat map from the Conditional formatting drop-down to emphasize the highest frequency counts.

It is also possible to summarize numerical variables. Select FreqMut from the Numerical variables drop-down. This will create the table shown below. Just as in the View tab you can sort the table by clicking on the column headers. You can also use sliders (e.g., click in the input box below I1) to limit the view to values in a specified range. To view only information for CNA with 0 or -1 levels click in the input box below the CNA header.

You can also create a bar chart based on the generated table (see image above). To download the table to csv format or the plot to a png format click the download icon on the right.

Filter

Use the Filter box to select (or omit) specific sets of rows from the data. See the help file for Data > View for details.

kmezhoud/bioCancer documentation built on Feb. 17, 2024, 10:29 a.m.