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Plot Reference and Query Cell Types using MDS

Source: R/plotCellTypeMDS.R
plotCellTypeMDS.Rd

This function facilitates the assessment of similarity between reference and query datasets through Multidimensional Scaling (MDS) scatter plots. It allows the visualization of cell types, color-coded with user-defined custom colors, based on a dissimilarity matrix computed from a user-selected gene set. If MDS coordinates are precomputed in reducedDims, they will be used; otherwise, MDS will be computed from scratch.

Usage

plotCellTypeMDS(
  query_data,
  reference_data,
  query_cell_type_col,
  ref_cell_type_col,
  cell_types = NULL,
  assay_name = "logcounts",
  max_cells_query = 5000,
  max_cells_ref = 5000
)

Arguments

query_data

A SingleCellExperiment containing the single-cell expression data and metadata.

reference_data

A SingleCellExperiment object containing the single-cell expression data and metadata.

query_cell_type_col

The column name in the colData of query_data that identifies the cell types.

ref_cell_type_col

The column name in the colData of reference_data that identifies the cell types.

cell_types

A character vector specifying the cell types to include in the plot. If NULL, all cell types are included.

assay_name

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

max_cells_query

Maximum number of query cells to retain after cell type filtering. If NULL, no downsampling of query cells is performed. Default is 5000.

max_cells_ref

Maximum number of reference cells to retain after cell type filtering. If NULL, no downsampling of reference cells is performed. Default is 5000.

Value

A ggplot object representing the MDS scatter plot with cell type coloring.

Details

The function first checks if MDS coordinates are available in the reducedDims of both datasets. If precomputed MDS is found, it uses those coordinates directly for visualization.

If MDS is not precomputed, the function selects specific subsets of cells from both reference and query datasets. It then calculates Spearman correlations between gene expression profiles, deriving a dissimilarity matrix. This matrix undergoes Classical Multidimensional Scaling (MDS) for visualization, presenting cell types in a scatter plot, distinguished by colors defined by the user.

References

  • Kruskal, J. B. (1964). "Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis". *Psychometrika*, 29(1), 1-27. doi:10.1007/BF02289565.

  • Borg, I., & Groenen, P. J. F. (2005). *Modern multidimensional scaling: Theory and applications* (2nd ed.). Springer Science & Business Media. doi:10.1007/978-0-387-25975-1.

Author

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

Examples

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

# Generate the MDS scatter plot with cell type coloring
mds_plot <- plotCellTypeMDS(query_data = query_data,
                            reference_data = reference_data,
                            cell_types = c("CD4", "CD8", "B_and_plasma", "Myeloid")[1:4],
                            query_cell_type_col = "SingleR_annotation",
                            ref_cell_type_col = "expert_annotation")
#> Computing MDS from expression data.
mds_plot