# scDataviz: single cell dataviz and downstream analyses

## Documentation for package ‘scDataviz’ version 1.23.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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.