Author: Matt Mulè

# Normalizing ADTs for datasets without empty droplets with the dsb function ModelNegativeADTnorm

#### Matt Mulè

In the functions below, recommend setting fast.km = TRUE for 10-fold faster compute times, see new vignette

Sometimes empty droplets are not available. In Supplementary Figure 1, we show that the fitted background population mean of each protein across all cells was concordant with the mean of ambient ADTs in both empty droplets and unstained control cells.

This experiment suggests that this fitted background mean captures an estimate of ambient noise. By log + 1 transforming ADTs across cells, fitting the background population mean with a Gaussian Mixture and subtracting this value from cells, we should partly remove the ambient component and 0-center the background population for each ADT. We can then implement step II exactly as in the dsb function `DSBNormalizeProtein`. We provide this method with the function `ModelNegativeADTnorm`.

    library(dsb)
    # Specify isotype controls to use in step II
    isotypes = c("MouseIgG1kappaisotype_PROT", "MouseIgG2akappaisotype_PROT",
                 "Mouse IgG2bkIsotype_PROT", "RatIgG2bkIsotype_PROT")

    # run ModelNegativeADTnorm to model ambient noise and implement step II
    raw.adt.matrix = dsb::cells_citeseq_mtx
    norm.adt = ModelNegativeADTnorm(cell_protein_matrix = raw.adt.matrix,
                                    denoise.counts = TRUE,
                                    use.isotype.control = TRUE,
                                    isotype.control.name.vec = isotypes
                                    )
    #> [1] "fitting models to each cell for dsb technical component and removing cell to cell technical noise"

We retain trimodal distributions of CD4 with the background population centered at 0. All populations are nicely recovered with concordant distribution of values as the default dsb method.

    par(mfrow = c(2,2)); r = '#009ACD80'
    lab = 'ModelNegativeADTnorm'
    hist(norm.adt["CD4_PROT", ], breaks = 45, col = r, main = 'CD4', xlab = lab)
    hist(norm.adt["CD8_PROT", ], breaks = 45, col = r, main = 'CD8', xlab = lab)
    hist(norm.adt["CD19_PROT", ], breaks = 45, col = r, main = 'CD19', xlab = lab)
    hist(norm.adt["CD18_PROT", ], breaks = 45, col = r, main = 'CD18', xlab = lab)

Note that two proteins in this 87 protein panel are expected to be expressed by every cell–HLA-ABC and CD18. cells with the lowest expression of ubiquitously expressed proteins can fall around 0 with this method. Relative CD18 values above are the same as the default dsb, however, the lowest population cells with this method are around 0.

Clustering performance and modeling e.g. with protein or joint WNN clustering is highly concordant using the default dsb and this modeled background method.

    # these data were installed with the SeuratData package
    # devtools::install_github('satijalab/seurat-data')
    # library(SeuratData)
    # InstallData(ds = 'bmcite') from https://doi.org/10.1016/j.cell.2019.05.031
    # load bone marrow CITE-seq data
    data('bmcite')
    bm = bmcite; rm(bmcite)

    # Extract raw bone marrow ADT data
    adt = GetAssayData(bm, slot = 'counts', assay = 'ADT')

    # unfortunately this data does not have isotype controls
    dsb.norm = ModelNegativeADTnorm(cell_protein_matrix = adt,
                                    denoise.counts = TRUE,
                                    use.isotype.control = FALSE)

Above we removed technical cell to cell variations with each cells fitted background only–adding isotype controls will further improve the precision in the technical component estimation. Note, if this dataset included isotype controls we would have used the following options:

    # specify isotype controls
    isotype.controls = c('isotype1', 'isotype 2')
    # normalize ADTs
    dsb.norm.2 = ModelNegativeADTnorm(cell_protein_matrix = adt,
                                      denoise.counts = TRUE,
                                      use.isotype.control = TRUE,
                                      isotype.control.name.vec = isotype.controls
                                      )

Examine protein expression distributions:

    library(ggplot2); theme_set(theme_bw())
    plist = list(geom_vline(xintercept = 0, color = 'red'),
                 geom_hline(yintercept = 0, color = 'red'),
                 geom_point(size = 0.2, alpha = 0.1))
    d = as.data.frame(t(dsb.norm))

    # plot distributions
    p1 = ggplot(d, aes(x = CD4, y = CD8a)) + plist
    p2 = ggplot(d, aes(x = CD19, y = CD3)) + plist
    cowplot::plot_grid(p1,p2)

Example downstream multimodal clustering using Seurat. The normalized valuse are added to the object directly without normalization within Seurat.

    bm = SetAssayData(bmcite, slot = 'data',
                      assay = 'ADT',
                      new.data = dsb.norm)

    # process RNA for WNN
    DefaultAssay(bm) <- 'RNA'
    bm <- NormalizeData(bm) %>%
      FindVariableFeatures() %>%
      ScaleData() %>%
      RunPCA()

    # process ADT for WNN # see the main dsb vignette for an alternate version
    DefaultAssay(bm) <- 'ADT'
    VariableFeatures(bm) <- rownames(bm[["ADT"]])
    bm = bm %>% ScaleData() %>% RunPCA(reduction.name = 'apca')

    # run WNN
    bm <- FindMultiModalNeighbors(
      bm, reduction.list = list("pca", "apca"),
      dims.list = list(1:30, 1:18), modality.weight.name = "RNA.weight"
    )

    bm <- FindClusters(bm, graph.name = "wsnn",
                       algorithm = 3, resolution = 2,
                       verbose = FALSE)
    bm <- RunUMAP(bm, nn.name = "weighted.nn",
                  reduction.name = "wnn.umap",
                  reduction.key = "wnnUMAP_")

    p2 <- DimPlot(bm, reduction = 'wnn.umap',
                  group.by = 'celltype.l2',
                  label = TRUE, repel = TRUE,
                  label.size = 2.5) + NoLegend()
    p2