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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 and will automatically open in the data viewer for modification. 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 that have clonotype5. Clonotype 5 is made of two compositions (a frequency of four for clonotype5 from the V(D)J node) with a Chain, V gene, D gene, and J gene as seen below the bars and by hovering. 

• 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 . In this example, 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 . An example of this would be clonotype1 when comparing the figure above and below). 

Tips for Figure Making

• When overlaying the Clonotype ID on plots from the Single cell counts analysis pipeline (such as the 3D Scatter plot example below), make sure that to use the Clonotype ID from the Single cell counts node and not the VDJ node is used. 

• B cell isotypes are defined by the Chain and C gene. In the examples below, the Chain and C gene are plotted by Barcode frequency using a Bar chart. On the top, no selection and filtering have been performed. On the second plot, the data has been selected and filtered by the heavy chain. By using Select & filter, certain Certain criteria can be focused on by using Select & filter. The third plot is stacked to 100% and colored by the V gene because the V regions do not change specificity during isotype switching. 

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