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• The example below shows the results from the Clonotype Frequency Plot task which is accessed by choosing to perform this task from the Single cell V(D)J node then modified in the data viewer. In this case, the barcode frequency is the number of clonotypes per cell because the barcode usually represents a single cell, so there are two cells which have clonotype 5 clonotype5 (purple bar with information from hovering) and clonotype 5 is made of two compositions (a frequency of four for clonotype 5 clonotype5 from the V(D)J node) witnessed by the Chain, V gene, D gene, and J gene seen below the bars and by hovering. 

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• Plotting Clonotype ID frequency, as seen below, for the gene expression node (Cell counts as the top bar chart) and VDJ node (VDJ counts as the bottom bar chart), highlights the difference between the two nodes (where the top plot is the number of cells per clonotype and the bottom plot is the number of V(D)J clonotypes present). Note that Cell Ranger does not always call the barcode as a cell and this can affect these frequencies when making comparisons between cell frequency per clonotype and barcode frequency per clonotype (an example of this would be clonotype1 when comparing the figure above and below). 

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