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 = FALSE
)

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.

Value

a ggplot object.


[Package MetaNeighbor version 1.13.0 Index]