User Friendly Single-Cell and Bulk RNA Sequencing Visualization

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Documentation for package ‘dittoSeq’ version 1.14.3

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

Help Pages

dittoSeq-package	dittoSeq
addDimReduction	Add any dimensionality reduction space to a SingleCellExperiment object containing bulk or single-cell data
addPrcomp	Add a prcomp pca calculation to a SingleCellExperiment object containing bulk or single-cell data
Darken	Darkens input colors by a set amount
demux.calls.summary	Plots the number of annotations per sample, per lane
demux.SNP.summary	Plots the number of SNPs sequenced per droplet
demuxlet.example	demuxlet.example
dittoBarPlot	Outputs a stacked bar plot to show the percent composition of samples, groups, clusters, or other groupings
dittoBoxPlot	Plots continuous data for customizeable cells'/samples' groupings on a y- (or x-) axis
dittoColors	Extracts the dittoSeq default colors
dittoDimHex	Show RNAseq data, grouped into hexagonal bins, on a scatter or dimensionality reduction plot
dittoDimPlot	Shows data overlayed on a tsne, pca, or similar type of plot
dittoDotPlot	Compact plotting of per group summaries for expression of multiple features
dittoFreqPlot	Plot cell type/cluster/identity frequencies per sample and per grouping
dittoHeatmap	Outputs a heatmap of given genes
dittoHex	Show RNAseq data, grouped into hexagonal bins, on a scatter or dimensionality reduction plot
dittoPlot	Plots continuous data for customizeable cells'/samples' groupings on a y- (or x-) axis
dittoPlotVarsAcrossGroups	Generates a dittoPlot where data points are genes/metadata summaries, per groups, instead of individual values per cells/samples.
dittoRidgeJitter	Plots continuous data for customizeable cells'/samples' groupings on a y- (or x-) axis
dittoRidgePlot	Plots continuous data for customizeable cells'/samples' groupings on a y- (or x-) axis
dittoScatterHex	Show RNAseq data, grouped into hexagonal bins, on a scatter or dimensionality reduction plot
dittoScatterPlot	Show RNAseq data overlayed on a scatter plot
dittoSeq	dittoSeq
gene	Returns the expression values of a gene for all cells/samples
getGenes	Returns the names of all genes of a target object.
getMetas	Returns the names of all meta.data slots of a target object.
getReductions	Returns the names of all dimensionality reduction slots of a target object.
importDemux	Extracts Demuxlet information into a pre-made SingleCellExperiment or Seurat object
importDittoBulk	import bulk sequencing data into a SingleCellExperiment format that will work with other dittoSeq functions.
isBulk	Retrieve whether a given object would be treated as bulk versus single-cell by dittoSeq
isGene	Tests if input is the name of a gene in a target object.
isMeta	Tests if an input is the name of a meta.data slot in a target object.
Lighten	Lightens input colors by a set amount
meta	Returns the values of a meta.data for all cells/samples
metaLevels	Gives the distinct values of a meta.data slot (or ident)
multi_dittoDimPlot	Generates dittoDimPlots for multiple features.
multi_dittoDimPlotVaryCells	Generates multiple dittoDimPlots, for a single feature, where each showing different cells
multi_dittoPlot	Generates dittoPlots for multiple features.
setBulk	Set whether a SingleCellExperiment object should be treated as bulk versus single-cell by dittoSeq
setBulk-method	Set whether a SingleCellExperiment object should be treated as bulk versus single-cell by dittoSeq
Simulate	Simulates what a colorblind person would see for any dittoSeq plot!