Plot Reference and Query Cell Types using MDS

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.

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

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".

Value

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

Details

To evaluate dataset similarity, 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")
mds_plot