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We will start with the protein data. We will normalize this data using Centered log-ratio (CLR). CLR was used to normalize antibody capture protein counts data in the paper that introduced CITE-Seq (Stoeckius et al. 2017) Seq [1] and in subsequent publications on similar assays (Stoeckius et al. 2018, Mimitou et al. 2018). [2. 3]. CLR normalization includes the following steps: Add 1, Divide by Geometric mean, Add 1, log base e.

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• Click the Merged counts data node
• Click Exploratory analysis in the toolbox
• Click Scatter plot
• Click Finish to run 
• Double-click the Scatter plot task node to open it
• Click 2D to switch to a 2D plot style (Figure 19)
  

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References

[1] Stoeckius, M., Hafemeister, C., Stephenson, W., Houck-Loomis, B., Chattopadhyay, P. K., Swerdlow, H., ... & Smibert, P. (2017). Simultaneous epitope and transcriptome measurement in single cells. Nature methods, 14(9), 865.

[2] Stoeckius, M., Zheng, S., Houck-Loomis, B., Hao, S., Yeung, B. Z., Mauck, W. M., ... & Satija, R. (2018). Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Genome biology, 19(1), 224.

[3] Mimitou, E., Cheng, A., Montalbano, A., Hao, S., Stoeckius, M., Legut, M., ... & Satija, R. (2018). Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay. bioRxiv, 466466.