An introduction to scReClassify package (original) (raw)

Dimension reduction

Prior to running scReClassify, we perform dimension reduction. matPCs is a tool in scReClassify to simplify this process. In this function, a dimension reduced matrix is returned with n principal components (PCs), where n is the number of principal components (PCs) that by sum explains at least 70% variance.

The function accepts either a matrix or a SingleCellExperiment object. If the data parameter is a SingleCellExperiment object, an assay variable must be specified to perform dimension reduction on the correct assay. If theSingleCellExperiment object data already has a ‘PCA’ in reducedDimNames(), the ‘PCA’ matrix of n columns are returned.

reducedDim(dat, "matPCs") <- matPCs(dat, assay = "logNorm", 0.7)

Synthetic noise (Demonstration purpose)

Here in this example, we will synthetically generate varying degree of noise (10-50%) in sample labels. The purpose here is to simulate different level of mislabeling in the data. Given a cell type label cls.truth, noisyClsfunction will randomly select a rho percentage of cells from a given cell type and relabel to other cell types.

Here, we create different degree of noise from 10% to 50%.

lab <- cellTypes

set.seed(1)
# Function to create noise in the cell type label
noisyCls <- function(dat, rho, cls.truth){
    cls.noisy <- cls.truth
    names(cls.noisy) <- colnames(dat)
    
    for(i in seq_len(length(table(cls.noisy)))) {
        # class label starts from 0
        if (i != length(table(cls.noisy))) {
            cls.noisy[sample(which(cls.truth == names(table(cls.noisy))[i]), 
                            floor(sum(cls.truth == names(table(cls.noisy))[i])*
                            rho))] <- names(table(cls.noisy))[i+1]
        } else {
            cls.noisy[sample(which(cls.truth == names(table(cls.noisy))[i]), 
                            floor(sum(cls.truth == names(table(cls.noisy))[i])*
                            rho))] <- names(table(cls.noisy))[1]
        }
    }
  
    print(sum(cls.truth != cls.noisy))
    return(cls.noisy)
}

cls.noisy01 <- noisyCls(t(reducedDim(dat, "matPCs")), rho=0.1, lab)

## [1] 34

cls.noisy02 <- noisyCls(t(reducedDim(dat, "matPCs")), rho=0.2, lab)

## [1] 71

cls.noisy03 <- noisyCls(t(reducedDim(dat, "matPCs")), rho=0.3, lab)

## [1] 108

cls.noisy04 <- noisyCls(t(reducedDim(dat, "matPCs")), rho=0.4, lab)

## [1] 144

cls.noisy05 <- noisyCls(t(reducedDim(dat, "matPCs")), rho=0.5, lab)

## [1] 182

With noisyCls function, we have relabeled Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Hepatoblast, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Macrophage, Erythrocyte, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Megakaryocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Erythrocyte, Hepatoblast, Megakaryocyte, Erythrocyte, Erythrocyte, Erythrocyte, Megakaryocyte, Endothelial Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Endothelial Cell, Erythrocyte, Macrophage, Mesenchymal Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Megakaryocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Macrophage, Hepatoblast, Mesenchymal Cell, Erythrocyte, Macrophage, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Erythrocyte, Megakaryocyte, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Megakaryocyte, Megakaryocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Mesenchymal Cell, Erythrocyte, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Erythrocyte, Macrophage, Mesenchymal Cell, Erythrocyte, Mesenchymal Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Hepatoblast, Endothelial Cell, Endothelial Cell, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Hepatoblast, Erythrocyte, Megakaryocyte, Megakaryocyte, Macrophage, Erythrocyte, Macrophage, Erythrocyte, Megakaryocyte, Hepatoblast, Macrophage, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Mesenchymal Cell, Endothelial Cell, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Megakaryocyte, Endothelial Cell, Megakaryocyte, Erythrocyte, Mesenchymal Cell, Hepatoblast, Endothelial Cell, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Mesenchymal Cell, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Macrophage, Hepatoblast, Erythrocyte, Hepatoblast, Endothelial Cell, Erythrocyte, Macrophage, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Mesenchymal Cell, Hepatoblast, Hepatoblast, Endothelial Cell, Endothelial Cell, Megakaryocyte, Hepatoblast, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Macrophage, Erythrocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Macrophage, Macrophage, Hepatoblast, Erythrocyte, Macrophage, Megakaryocyte, Erythrocyte, Hepatoblast, Macrophage, Macrophage, Endothelial Cell, Megakaryocyte, Endothelial Cell, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Endothelial Cell, Hepatoblast, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Macrophage, Erythrocyte, Hepatoblast, Macrophage, Hepatoblast, Mesenchymal Cell, Erythrocyte, Erythrocyte, Megakaryocyte, Hepatoblast, Macrophage, Hepatoblast, Endothelial Cell, Mesenchymal Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Macrophage, Macrophage, Hepatoblast, Erythrocyte, Erythrocyte, Mesenchymal Cell, Macrophage, Macrophage, Erythrocyte, Erythrocyte, Macrophage, Hepatoblast, Hepatoblast, Macrophage, Macrophage, Megakaryocyte, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Hepatoblast, Erythrocyte, Macrophage, Megakaryocyte, Macrophage, Endothelial Cell, Erythrocyte, Macrophage, Endothelial Cell, Macrophage, Hepatoblast, Endothelial Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Hepatoblast, Megakaryocyte, Macrophage, Megakaryocyte, Megakaryocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Macrophage, Macrophage, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Hepatoblast, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Macrophage, Erythrocyte, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Megakaryocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Erythrocyte, Hepatoblast, Megakaryocyte, Erythrocyte, Erythrocyte, Erythrocyte, Megakaryocyte, Endothelial Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Endothelial Cell, Erythrocyte, Macrophage, Mesenchymal Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Megakaryocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Macrophage, Hepatoblast, Mesenchymal Cell, Erythrocyte, Macrophage, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Erythrocyte, Megakaryocyte, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Megakaryocyte, Megakaryocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Mesenchymal Cell, Erythrocyte, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Erythrocyte, Macrophage, Mesenchymal Cell, Erythrocyte, Mesenchymal Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Hepatoblast, Endothelial Cell, Endothelial Cell, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Hepatoblast, Erythrocyte, Megakaryocyte, Megakaryocyte, Macrophage, Erythrocyte, Macrophage, Erythrocyte, Megakaryocyte, Hepatoblast, Macrophage, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Mesenchymal Cell, Endothelial Cell, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Megakaryocyte, Endothelial Cell, Megakaryocyte, Erythrocyte, Mesenchymal Cell, Hepatoblast, Endothelial Cell, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Mesenchymal Cell, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Macrophage, Hepatoblast, Erythrocyte, Hepatoblast, Endothelial Cell, Erythrocyte, Macrophage, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Mesenchymal Cell, Hepatoblast, Hepatoblast, Endothelial Cell, Endothelial Cell, Megakaryocyte, Hepatoblast, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Macrophage, Erythrocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Macrophage, Macrophage, Hepatoblast, Erythrocyte, Macrophage, Megakaryocyte, Erythrocyte, Hepatoblast, Macrophage, Macrophage, Endothelial Cell, Megakaryocyte, Endothelial Cell, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Endothelial Cell, Hepatoblast, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Macrophage, Erythrocyte, Hepatoblast, Macrophage, Hepatoblast, Mesenchymal Cell, Erythrocyte, Erythrocyte, Megakaryocyte, Hepatoblast, Macrophage, Hepatoblast, Endothelial Cell, Mesenchymal Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Macrophage, Macrophage, Hepatoblast, Erythrocyte, Erythrocyte, Mesenchymal Cell, Macrophage, Macrophage, Erythrocyte, Erythrocyte, Macrophage, Hepatoblast, Hepatoblast, Macrophage, Macrophage, Megakaryocyte, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Hepatoblast, Erythrocyte, Macrophage, Megakaryocyte, Macrophage, Endothelial Cell, Erythrocyte, Macrophage, Endothelial Cell, Macrophage, Hepatoblast, Endothelial Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Hepatoblast, Megakaryocyte, Macrophage, Megakaryocyte, Megakaryocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Macrophage, Macrophage, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Hepatoblast, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Macrophage, Erythrocyte, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Megakaryocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Erythrocyte, Hepatoblast, Megakaryocyte, Erythrocyte, Erythrocyte, Erythrocyte, Megakaryocyte, Endothelial Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Endothelial Cell, Erythrocyte, Macrophage, Mesenchymal Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Megakaryocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Macrophage, Hepatoblast, Mesenchymal Cell, Erythrocyte, Macrophage, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Erythrocyte, Megakaryocyte, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Megakaryocyte, Megakaryocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Mesenchymal Cell, Erythrocyte, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Erythrocyte, Macrophage, Mesenchymal Cell, Erythrocyte, Mesenchymal Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Hepatoblast, Endothelial Cell, Endothelial Cell, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Hepatoblast, Erythrocyte, Megakaryocyte, Megakaryocyte, Macrophage, Erythrocyte, Macrophage, Erythrocyte, Megakaryocyte, Hepatoblast, Macrophage, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Mesenchymal Cell, Endothelial Cell, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Megakaryocyte, Endothelial Cell, Megakaryocyte, Erythrocyte, Mesenchymal Cell, Hepatoblast, Endothelial Cell, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Mesenchymal Cell, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Macrophage, Hepatoblast, Erythrocyte, Hepatoblast, Endothelial Cell, Erythrocyte, Macrophage, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Mesenchymal Cell, Hepatoblast, Hepatoblast, Endothelial Cell, Endothelial Cell, Megakaryocyte, Hepatoblast, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Macrophage, Erythrocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Macrophage, Macrophage, Hepatoblast, Erythrocyte, Macrophage, Megakaryocyte, Erythrocyte, Hepatoblast, Macrophage, Macrophage, Endothelial Cell, Megakaryocyte, Endothelial Cell, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Endothelial Cell, Hepatoblast, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Macrophage, Erythrocyte, Hepatoblast, Macrophage, Hepatoblast, Mesenchymal Cell, Erythrocyte, Erythrocyte, Megakaryocyte, Hepatoblast, Macrophage, Hepatoblast, Endothelial Cell, Mesenchymal Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Macrophage, Macrophage, Hepatoblast, Erythrocyte, Erythrocyte, Mesenchymal Cell, Macrophage, Macrophage, Erythrocyte, Erythrocyte, Macrophage, Hepatoblast, Hepatoblast, Macrophage, Macrophage, Megakaryocyte, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Hepatoblast, Erythrocyte, Macrophage, Megakaryocyte, Macrophage, Endothelial Cell, Erythrocyte, Macrophage, Endothelial Cell, Macrophage, Hepatoblast, Endothelial Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Hepatoblast, Megakaryocyte, Macrophage, Megakaryocyte, Megakaryocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Macrophage, Macrophage, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Hepatoblast, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Macrophage, Erythrocyte, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Megakaryocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Erythrocyte, Hepatoblast, Megakaryocyte, Erythrocyte, Erythrocyte, Erythrocyte, Megakaryocyte, Endothelial Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Endothelial Cell, Erythrocyte, Macrophage, Mesenchymal Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Megakaryocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Macrophage, Hepatoblast, Mesenchymal Cell, Erythrocyte, Macrophage, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Erythrocyte, Megakaryocyte, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Megakaryocyte, Megakaryocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Mesenchymal Cell, Erythrocyte, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Erythrocyte, Macrophage, Mesenchymal Cell, Erythrocyte, Mesenchymal Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Hepatoblast, Endothelial Cell, Endothelial Cell, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Hepatoblast, Erythrocyte, Megakaryocyte, Megakaryocyte, Macrophage, Erythrocyte, Macrophage, Erythrocyte, Megakaryocyte, Hepatoblast, Macrophage, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Mesenchymal Cell, Endothelial Cell, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Megakaryocyte, Endothelial Cell, Megakaryocyte, Erythrocyte, Mesenchymal Cell, Hepatoblast, Endothelial Cell, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Mesenchymal Cell, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Macrophage, Hepatoblast, Erythrocyte, Hepatoblast, Endothelial Cell, Erythrocyte, Macrophage, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Mesenchymal Cell, Hepatoblast, Hepatoblast, Endothelial Cell, Endothelial Cell, Megakaryocyte, Hepatoblast, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Macrophage, Erythrocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Macrophage, Macrophage, Hepatoblast, Erythrocyte, Macrophage, Megakaryocyte, Erythrocyte, Hepatoblast, Macrophage, Macrophage, Endothelial Cell, Megakaryocyte, Endothelial Cell, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Endothelial Cell, Hepatoblast, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Macrophage, Erythrocyte, Hepatoblast, Macrophage, Hepatoblast, Mesenchymal Cell, Erythrocyte, Erythrocyte, Megakaryocyte, Hepatoblast, Macrophage, Hepatoblast, Endothelial Cell, Mesenchymal Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Macrophage, Macrophage, Hepatoblast, Erythrocyte, Erythrocyte, Mesenchymal Cell, Macrophage, Macrophage, Erythrocyte, Erythrocyte, Macrophage, Hepatoblast, Hepatoblast, Macrophage, Macrophage, Megakaryocyte, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Hepatoblast, Erythrocyte, Macrophage, Megakaryocyte, Macrophage, Endothelial Cell, Erythrocyte, Macrophage, Endothelial Cell, Macrophage, Hepatoblast, Endothelial Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Hepatoblast, Megakaryocyte, Macrophage, Megakaryocyte, Megakaryocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Macrophage, Macrophage, Erythrocyte and Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Hepatoblast, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Macrophage, Erythrocyte, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Megakaryocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Mesenchymal Cell, Endothelial Cell, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Erythrocyte, Hepatoblast, Megakaryocyte, Erythrocyte, Erythrocyte, Erythrocyte, Megakaryocyte, Endothelial Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Endothelial Cell, Erythrocyte, Macrophage, Mesenchymal Cell, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Macrophage, Megakaryocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Macrophage, Hepatoblast, Mesenchymal Cell, Erythrocyte, Macrophage, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Mesenchymal Cell, Mesenchymal Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Hepatoblast, Mesenchymal Cell, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Erythrocyte, Megakaryocyte, Endothelial Cell, Mesenchymal Cell, Mesenchymal Cell, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Megakaryocyte, Megakaryocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Mesenchymal Cell, Erythrocyte, Endothelial Cell, Erythrocyte, Mesenchymal Cell, Erythrocyte, Macrophage, Mesenchymal Cell, Erythrocyte, Mesenchymal Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Hepatoblast, Endothelial Cell, Endothelial Cell, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Hepatoblast, Erythrocyte, Megakaryocyte, Megakaryocyte, Macrophage, Erythrocyte, Macrophage, Erythrocyte, Megakaryocyte, Hepatoblast, Macrophage, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Mesenchymal Cell, Endothelial Cell, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Megakaryocyte, Endothelial Cell, Megakaryocyte, Erythrocyte, Mesenchymal Cell, Hepatoblast, Endothelial Cell, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Mesenchymal Cell, Erythrocyte, Hepatoblast, Erythrocyte, Endothelial Cell, Macrophage, Hepatoblast, Erythrocyte, Hepatoblast, Endothelial Cell, Erythrocyte, Macrophage, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Mesenchymal Cell, Hepatoblast, Hepatoblast, Endothelial Cell, Endothelial Cell, Megakaryocyte, Hepatoblast, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Macrophage, Erythrocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Macrophage, Macrophage, Hepatoblast, Erythrocyte, Macrophage, Megakaryocyte, Erythrocyte, Hepatoblast, Macrophage, Macrophage, Endothelial Cell, Megakaryocyte, Endothelial Cell, Hepatoblast, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Endothelial Cell, Hepatoblast, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Macrophage, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Erythrocyte, Hepatoblast, Macrophage, Erythrocyte, Hepatoblast, Macrophage, Hepatoblast, Mesenchymal Cell, Erythrocyte, Erythrocyte, Megakaryocyte, Hepatoblast, Macrophage, Hepatoblast, Endothelial Cell, Mesenchymal Cell, Hepatoblast, Erythrocyte, Mesenchymal Cell, Macrophage, Macrophage, Hepatoblast, Erythrocyte, Erythrocyte, Mesenchymal Cell, Macrophage, Macrophage, Erythrocyte, Erythrocyte, Macrophage, Hepatoblast, Hepatoblast, Macrophage, Macrophage, Megakaryocyte, Macrophage, Erythrocyte, Endothelial Cell, Macrophage, Hepatoblast, Erythrocyte, Macrophage, Megakaryocyte, Macrophage, Endothelial Cell, Erythrocyte, Macrophage, Endothelial Cell, Macrophage, Hepatoblast, Endothelial Cell, Endothelial Cell, Hepatoblast, Erythrocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Hepatoblast, Megakaryocyte, Macrophage, Megakaryocyte, Megakaryocyte, Erythrocyte, Macrophage, Erythrocyte, Erythrocyte, Hepatoblast, Erythrocyte, Erythrocyte, Erythrocyte, Endothelial Cell, Erythrocyte, Erythrocyte, Macrophage, Macrophage, Erythrocyte number of cells for rhoequal to 0.1, 0.2, 0.3, 0.4 and 0.5 respectively.

Use scReClassify to correct mislabeled cell types.

Here in this example, we will only use Support Vector machine (svm) as base classifier.

Benchmark evaluation

To benchmark scReClassify, we perform scReclassify to all degree of noise with 10 repeats. We measure the accuracy of scReClassify and the Adjusted Rand Index (ARI) to measure the concordance of the reclassified cell type to the true cell type label.

###################################
# SVM
###################################
base <- "svm"
set.seed(1)
result = lapply(seq_len(10), function(j) {
    final <- multiAdaSampling(dat, cls.noisy01, reducedDimName = "matPCs", 
                            classifier=base, percent=1, L=10)$final
    ari01 <- mclust::adjustedRandIndex(lab, final)
    acc01 <- bAccuracy(lab, final)
    
    final <- multiAdaSampling(dat, cls.noisy02, reducedDimName = "matPCs", 
                            classifier=base,  percent=1, L=10)$final
    ari02 <- mclust::adjustedRandIndex(lab, final)
    acc02 <- bAccuracy(lab, final)
    
    final <- multiAdaSampling(dat, cls.noisy03, reducedDimName = "matPCs", 
                            classifier=base, percent=1, L=10)$final
    ari03 <- mclust::adjustedRandIndex(lab, final)
    acc03 <- bAccuracy(lab, final)
    
    final <- multiAdaSampling(dat, cls.noisy04, reducedDimName = "matPCs", 
                            classifier=base, percent=1, L=10)$final
    ari04 <- mclust::adjustedRandIndex(lab, final)
    acc04 <- bAccuracy(lab, final)
    
    final <- multiAdaSampling(dat, cls.noisy05, reducedDimName = "matPCs", 
                            classifier=base, percent=1, L=10)$final
    ari05 <- mclust::adjustedRandIndex(lab, final)
    acc05 <- bAccuracy(lab, final)
    
    c(
      acc01 = acc01,
      acc02 = acc02,
      acc03 = acc03,
      acc04 = acc04,
      acc05 = acc05,
      ari01 = ari01,
      ari02 = ari02,
      ari03 = ari03,
      ari04 = ari04,
      ari05 = ari05
    )
})

result = do.call(rbind, result)
acc = result[,seq_len(5)]
colnames(acc) = seq(from=0.1,to=0.5,by=0.1)

ari = result[,seq(from= 6, to = 10)]
colnames(ari) = seq(from=0.1,to=0.5,by=0.1)

We can visualise the performance of the scReClassify. The boxes represent the accuracy and the ARI after scReClassify. The red markers indicate the baseline (prior to scReClassify).

plot.new()
par(mfrow = c(1,2))
boxplot(acc, col="lightblue", main="SVM Accuracy", 
        ylim=c(0.45, 1), xlab = "rho", ylab = "Accuracy")
points(x=seq_len(5), y=c(
    bAccuracy(lab, cls.noisy01), 
    bAccuracy(lab, cls.noisy02),
    bAccuracy(lab, cls.noisy03), 
    bAccuracy(lab, cls.noisy04),
    bAccuracy(lab, cls.noisy05)), 
    col="red3", pch=c(2,3,4,5,6), cex=1)
boxplot(ari, col="lightblue", main="SVM ARI", 
        ylim=c(0.25, 1), xlab = "rho", ylab = "ARI")
points(x=seq_len(5), y=c(
    mclust::adjustedRandIndex(lab, cls.noisy01), 
    mclust::adjustedRandIndex(lab, cls.noisy02),
    mclust::adjustedRandIndex(lab, cls.noisy03), 
    mclust::adjustedRandIndex(lab, cls.noisy04),
    mclust::adjustedRandIndex(lab, cls.noisy05)), 
    col="red3", pch=c(2,3,4,5,6), cex=1)

The plot shows that with scReClassify, cell type information have been refined (boxes are higher than the red markers). The scReClassified results show higher accuracy across noise levels 0.1 - 0.4 (i.e. closer to the true label). With the noise level 0.5, it is showing similar accuracy which is as expected because the initial label contains equal amount of true and false information and thus making it difficult for the algorithm to learn the true label. This shows that scReClassify is also robust to noisy cell type labels.