plotDotPlot {MetaNeighbor} | R Documentation |
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 = FALSE )
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. |
a ggplot object.