# User Friendly Single-Cell and Bulk RNA Sequencing Visualization

## Documentation for package ‘dittoSeq’ version 1.22.0

- 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
GeneTargeting | Control of Gene/Feature targeting
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!