| basetheme | Package-wide, non-user function used to set a base 'ggplot2' theme. |
| clusKNN | A wrapper function for 'Seurat"s 'FindNeighbors' and 'FindClusters'. |
| contourPlot | Draw a contour plot, typically relating to co-ordinates of a 2-dimensional reduction / embedding, typically contained within a 'SingleCellExperiment' object. |
| downsampleByVar | Downsample an input data-frame or matrix based on variance. |
| importData | Import a data-frame or matrix, and associated metadata, to a 'SingleCellExperiment' object. |
| markerEnrichment | Find enriched markers per identified cluster and calculate cluster abundances across these for samples and metadata variables. |
| markerExpression | Highlight the individual marker expression profile across a 2-dimensional reduction / embedding, typically contained within a 'SingleCellExperiment' object. By default, this function plots the expression profile of 6 randomly-selected markers from your data. |
| markerExpressionPerCluster | Generate box-and-whisker plots illustrating marker expression per k-NN identified cluster. By default, 5 randomly-selected clusters are selected, and the expression profiles of 10 randomly-selected markers are plot across these. |
| metadataPlot | Colour shade a 2-dimensional reduction / embedding based on metadata, typically contained within a 'SingleCellExperiment' object. |
| performUMAP | Perform UMAP on an input data-frame or matrix, or 'SingleCellExperiment' object, using the basic R implementation of UMAP. |
| plotClusters | Highlight cell-to-cluster assignments across a 2-dimensional reduction / embedding. |
| plotSignatures | Find enriched markers per identified cluster and visualise these as a custom corrplot. |
| processFCS | Input, filter, normalise, and transform FCS expression data. |