Figure 3:

(a)-(c) Batch effect removal. 4K cells were subsampled from two single-cell mass cytometry immune profiles on blood samples of two patients infected with Dengue fever. Top: Both patients exhibit heightened IFNγ (x-axis), a pro-inflammatory cytokine associated with TNFα (y-axis) Bottom: IFNγ histograms for each batch. (a) Data before denoising. (b) Denoising of unaligned data enhances a technical effect between samples in IFNγ. (c) Harmonic alignment corrects the IFNγ shift. (d) Multimodal data fusion. Overlap of cell neighborhoods from joint gene expression and chromatin profiling of single cells. Harmonic alignment most accurately recovers the pointwise relationship between the manifolds.