plotDotPlot: Plot dot plot showing expression of a gene set across cell...
In MetaNeighbor: Single cell replicability analysis

The size of each dot reflects the number of cell that express a gene, the color reflects the average expression. Expression of genes is first average and scaled in each dataset independently. The final value is obtained by averaging across datasets.

plotDotPlot(
  dat,
  experiment_labels,
  celltype_labels,
  gene_set,
  i = 1,
  normalize_library_size = TRUE,
  alpha_row = 10,
  average_expressing_only = TRUE
)

`dat`	A SummarizedExperiment object containing gene-by-sample expression matrix.
`experiment_labels`	A vector that indicates the source/dataset of each sample.
`celltype_labels`	A character vector that indicates the cell type of each sample.
`gene_set`	Gene set of interest provided as a vector of genes.
`i`	Default value 1; non-zero index value of assay containing the matrix data.
`normalize_library_size`	Whether to apply library size normalization before computing average expression (set this value to FALSE if data are already normalized).
`alpha_row`	Parameter controling row ordering: a higher value of alpha_row gives more weight to extreme AUROC values (close to 1).
`average_expressing_only`	Whether average expression should be computed based only on expressing cells (Seurat default) or taking into account zeros.