Cell Clonotypes tables

The Cell Clonotypes elements contain two table views, centered around the clonotypes (Image browse_clonotypes_16_n_p) and barcodes (Image browse_cells_16_n_p). Multiple clonotypes can be identified for a barcode, where each clonotype is for one chain. These are the cell-level clonotypes (Image browse_cells_16_n_p). Clonotypes (Image browse_clonotypes_16_n_p) can have more than one chain (see below). For a given chain, the clonotype consists of multiple cell-level clonotypes with the same characteristics. The different chains present in one clonotype are supported by the corresponding cell-level clonotypes being present in the same barcode.

Both views contain the following information (see figure 10.9):

Image cell_clonotypes_view
Figure 10.9: Views of the same TCR Cell Clonotypes element. Note that not all table columns are shown. Clonotype with number 9 is highlighted in both views. Top: View centered around the identified clonotypes, sorted after the number of barcodes. All identified chains for the clonotype are shown. For example, clonotype 9 contains both a TRA and TRB chain, while clonotypes 10 and 11 contain only a TRB and TRA chain, respectively. When a clonotype is selected, a second table lists the barcodes with the corresponding clonotype. Bottom: View centered around the barcodes, sorted by barcode. Rows with the same barcode have the same background color when the table is sorted after the barcode.

The view centered around the identified clonotypes additionally contains the numbers of barcodes with the given clonotype. Clicking on a row in this view opens a new table listing the corresponding barcodes (see figure 10.9).

The cell-level clonotypes view also provides (see figure 10.9):