Sample Info (Attributes) file
Sample information files includes Attributes files, Sample Mapping files, Attribute Color files, and files that combine information. These are tab-delimited text files with extension .txt. You load them as you would data files, via the File menu. IGV can load multiple sample information files per session.
When loaded into IGV, attributes display in a separate color-coded panel between sample names and tracks. See Sample Attributes and Sorting, Grouping, and Filtering for more information on displaying attributes and using attributes to manipulate tracks. IGV automatically assigns colors and heatmaps to attribute data values and what it determines are data ranges.
This page has the following sections.
Sample information files allow integrating diverse data tracks from the same sample or patient.
Consider your data visualization needs as the various sample information sets allow for different features of IGV. The decision tree table below matches use cases to the Sample Information file types.
Attribute, mapping, and color information may be in separate files, i.e. in Attributes files, Mapping files, and Color files, or in a single Sample Information file.
When loading attributes for datasets where sample names are identical across file types, no mapping information is necessary for the attributes to apply to the multiple data type tracks. However, to apply the same attribute information across datasets where sample names differ, you can use either of two different types of Sample Information sets as indicated by (b) and (c) in the table.
An Attributes file lists track identifiers in the first column and attributes in subsequent columns with a single header row. IGV matches the track identifiers in a data file with the track identifiers in the Attributes file.
For example, load the second example file on top of IGV hg19's CopyNumber: [genome_wide_snp_6__broad]. This data is found in the hosted server data The Cancer Genome Atlas>TCGA Broad GDAC>Firehose Standard Data>Broad Firehose Standard Data Run: 2015_02_04>BLCA-TP. Applying attributes to the data file allows sorting by copy number for the 22q13:32 loci and the pathology.M.stage attribute as shown in the Screenshot (2015.03.05) below.
Acceptable variations to the Attributes file
So long as the first row contains attribute labels and the first column sample names, the remaining rows may contain information pertaining to samples in any data type and be organized in any way.
In the case of different data sets with different sample names from the same individual, e.g. copy number and RNA expression, you may wish to apply the information within a single attributes file in duplicate to the different data types. In this case, you may (b) additionally load a Sample Mapping file as outlined in the next section or (c) modify your Attributes file as outlined below.
For a single attributes file, duplicate the attributes by copy-pasting into empty rows, then modify sample names in the first column as needed for the differentially named datasets.
For multiple attributes files, duplicate the entire file and open each to modify sample names for the differentially named datasets as needed.
The Modified Attributes file includes a column indicating a linking identifier for use in mutation overlay.
A Sample Mapping file links differential sample names to resolve disparities in sample naming within the Attributes file and the data files to which the attributes should apply. The file contains two tab-delimited columns.
Example 3 asks to download: BLCA_SampleMapping_3sets.txt
As with the Attributes file, information can be represented in a single or multiple Sample Mapping files.
By default, IGV randomly assigns colors to the attribute values. You can optionally specify the colors for attribute values in RGB format for a specific label, a specific value, or as a heatmap scale for numeric columns in monocolor or in two-color heatmap for specified ranges. Customize colors using either a separate Attribute Colors file or by adding a colors section to the end of a Sample Information file. Colors information is tab-delimited with three or four columns as shown in the example below.
Look up RGB values by color wheel at https://color.adobe.com/create/color-wheel/. Alternatively look up RGB values on a chart at http://www.rapidtables.com/web/color/RGB_Color.htm.
Briefly, RGB (red, green, and blue light) refers to a system of representing colors for computer display with zero representing absence and 255 giving maximum light for a color in comma-separated values. Example color RGB values are given below.