plotDotPlot {MetaNeighbor} | R Documentation

## Plot dot plot showing expression of a gene set across cell types.

### Description

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.

### Usage

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

### Arguments

`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.

[Package MetaNeighbor version 1.10.0 Index]