scDataviz: single cell dataviz and downstream analyses

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Documentation for package ‘scDataviz’ version 1.18.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.