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

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• B cell isotypes are defined by the Chain and C gene. In the examples below, Chain and C gene are plotted by Barcode frequency using a Bar chart. On the top, no selection and filtering has been performed. On the bottom plot, the heavy chain data has been selected and filtered by in the dataheavy chain. By using Select & filter, certain criteria can be selected and focused on. 

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• Below, CDR3 abundance is plotted by barcode frequency and colored by Clonotype ID in the top plot Bar chart. In the bottom example, the plot is instead colored by Chain and other modifications have been made , such as axis ticks and the number of groups per page, has been made. Note that the predicted CDR3 amino acid sequence is plotted here, but the predicted CDR3 nucleotide sequence (cdr3_nt) as well as information for other Complementarity-Determining Regions is also available. 

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• Gene usage plots for the V, D, and J genes can be plotted many ways, as seen by the Bar chart examples below for the V gene. In the top plot, barcode frequency for V genes is sorted by frequency in descending order and colored by Chain. The transposed plot below shows all of the groups sorted by ascending value and the heavy chain has been excluded. 

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• In the example below, a pie Pie chart split by Chain is used to plot the V gene and J gene. This is another way to explore and visualize frequency. 

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