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

Show data in table form

Choose one of the datasets from the Datasets dropdown. Files are loaded into bioCancer through the Manage tab.

By default all columns in the data are shown. Click on any variable to focus on it alone. To select several variables use the SHIFT and ARROW keys on your keyboard. On a mac the CMD key can also be used to select multiple variables. The same effect is achieved on windows using the CTRL key. To select all variable use CTRL-A (or CMD-A on mac).

By default only 10 rows of are shown at one time. You can change this setting through the Show ... entries dropdown. Press the Next and Previous buttons at the bottom-right of the screen to navigate through the data.

Click on a column header in the table to sort the data by the values of that variable. Clicking again will toggle between sorting in ascending and descending order. To sort on multiple columns at once press shift and then click on the 2nd, 3rd, etc. column to sort by.

There are several ways to select a subset of the data to view. The Filter box on the left (click the check-box first) can be used with > and < signs and you can also combine subset commands. For example, x > 3 & y == 2 would show only those rows for which the variable x has values larger than 3 and for which y has values equal to 2. Note that in R, and most other programming languages, = is used to assign a value and == to evaluate if the value of a variable is equal to some other value. In contrast != is used to determine if a variable is unequal to some value. You can also use expressions that have an or condition. For example, to select rows where mutation frequency is smaller than 20 and larger than 10 use FreqMut > 10 & FreqMut < 20. & is the symbol for and. The table below gives an overview of common operators.

You can also use string matching to select rows. For example, type grepl("lu", Diseases) to select rows with lung Cancers. This search is case sensitive by default. For case insensitive search you would use grepl("TCGA", name, ignore.case = TRUE). Type your statement in the Filter box and press return to see the result on screen or an error below the box if the expression is invalid.

It is important to note that these filters are persistent. A filter entered in one of the Data-tabs will also be applied to other tabs and to any analysis conducted through the bioCancer menus. To deactivate a filter uncheck the Filter check-box. To remove a filter simply erase it.

Operator Description Example `<` less than `price < 5000` `<=` less than or equal to `carat <= 2` `>` greater than `price > 1000` `>=` greater than or equal to `carat >= 2` `==` exactly equal to `cut == 'Fair'` `!=` not equal to `cut != 'Fair'` `|` x OR y `price > 10000 | cut == 'Premium'` `&` x AND y `carat < 2 & cut == 'Fair'` `%in%` x is one of y `cut %in% c('Fair', 'Good')`

For variables that have a limited number of different values (i.e., a factor) you can select the levels to keep from the column filter below the variable name. For example, to filter on rows with CNA = -1 click in the box below the CNA column header and select -1 from the dropdown menu shown. You can also type a string into these column filters followed by return. Note that matching is case-insensitive. In fact, typing 1 would produce the same result because the search will match any part of a string. Similarly, you can type a string to select observations for character variables (e.g., street names).

For numeric variables the column filter boxes have some special features that make them almost as powerful as the Filter box. For numerical and integer variables you can use ... to indicate a range. For example, to select mRNA values between 200 and 500 type 200 ... 500 and press return. The range is inclusive of the values typed. Furthermore, if we want to filter on FreqMut 20 ... will show only Studies with mutation frequancy larger than or equal to 20. Numeric variables also have a slider that you can use to define the range of values to keep.

If you want to get really fancy you can use the search box on the top right to search across all columns in the data using regular expressions. For example, to find all rows that have an entry in any column ending with the number 72 type 72$ (i.e., the $ sign is used to indicate the end of an entry). For all rows with entries that start with 60 use ^60 (i.e., the ^ is used to indicate the first character in an entry). Regular expressions are incredibly powerful for search but this is a big topic area. To learn more about regular expressions see this tutorial.

It is important to note that column sorting, column filters, and search are not persistent. To store these settings for use in other parts of bioCancer press the Store button. You can store the data and settings under a different dataset name by changing the value in the text input to the left of the Store button. This feature can also be used to select a subset of variables to keep. Just select the ones you want to keep and press the Store button. For more control over the variables you want to keep or remove and to specify their order in the dataset use the Tools > Transform tab.