Calculate Nearest Neighbor Diagnostics for Cell Type Classification

This function computes the probabilities for each query cell of belonging to either the reference or query dataset for each cell type using nearest neighbor analysis.

The S3 plot method generates a density plot showing the distribution of probabilities for each cell of belonging to either the reference or query dataset for each cell type.

calculateNearestNeighborProbabilities(
  query_data,
  reference_data,
  query_cell_type_col,
  ref_cell_type_col,
  cell_types = NULL,
  pc_subset = 1:5,
  n_neighbor = 20,
  assay_name = "logcounts"
)

# S3 method for class 'calculateNearestNeighborProbabilitiesObject'
plot(x, cell_types = NULL, ...)

Arguments

query_data

A SingleCellExperiment object containing numeric expression matrix for the query cells.

reference_data

A SingleCellExperiment object containing numeric expression matrix for the reference cells.

query_cell_type_col

A character string specifying the column name in the query dataset containing cell type annotations.

ref_cell_type_col

A character string specifying the column name in the reference dataset containing cell type annotations.

cell_types

A character vector specifying the cell types to include in the plot. If NULL, all cell types in x will be plotted. Default is NULL.

pc_subset

A vector specifying the subset of principal components to use in the analysis. Default is 1:5

n_neighbor

An integer specifying the number of nearest neighbors to consider. Default is 20.

assay_name

Name of the assay on which to perform computations. Default is "logcounts".

x

An object of class nearestNeighbotDiagnostics containing the probabilities calculated by the calculateNearestNeighborProbabilities function.

...

Additional arguments to be passed to geom_density.

Value

A list where each element corresponds to a cell type and contains:

n_neighbor

The number of nearest neighbors considered.

n_query

The number of cells in the query dataset for each cell type.

query_prob

The average probability of each query cell belonging to the reference dataset.

The list is assigned the class "calculateNearestNeighborProbabilities". Each element in the list is named after the respective cell type.

The S3 plot method returns a ggplot density plot.

Details

The function conducts PCA on both the query and reference datasets to reduce dimensionality. It then compares each query cell to its nearest neighbors in the reference dataset to estimate the probability of membership in each cell type. Sample sizes between datasets are balanced using data augmentation if necessary.

The S3 plot method creates a density plot to visualize the distribution of probabilities for each cell belonging to the reference or query dataset for each cell type. It utilizes the ggplot2 package for plotting.

See also

plot.calculateNearestNeighborProbabilitiesObject

calculateNearestNeighborProbabilities

Author

Anthony Christidis, anthony-alexander_christidis@hms.harvard.edu

Examples

# Load data
data("reference_data")
data("query_data")

# Project the query data onto PCA space of reference
nn_output <- calculateNearestNeighborProbabilities(query_data = query_data,
                                                   reference_data = reference_data,
                                                   query_cell_type_col = "SingleR_annotation",
                                                   ref_cell_type_col = "expert_annotation",
                                                   pc_subset = 1:10,
                                                   n_neighbor = 20)

# Plot output
plot(nn_output, cell_types = c("CD4", "CD8", "B_and_plasma", "Myeloid"))