Man pages for dtm2451/DittoSeq
User Friendly Single-Cell and Bulk RNA Sequencing Visualization

addDimReductionAdd any dimensionality reduction space to an RNAseq object
addMetaRNAseqAdd metadata slot to an RNAseq object
addPrcompAdd a prcomp pca calculation to an RNAseq object
DarkenDarkens input colors by a set amount
demux.calls.summaryPlots the number of annotations per sample, per lane
demuxlet.exampledemuxlet.example
demux.SNP.summaryPlots the number of SNPs sequenced per droplet
dittoBarPlotOutputs a stacked bar plot to show the percent composition of...
dittoColorsExtracts the dittoSeq default colors
dittoDimPlotShows data overlayed on a tsne, pca, or similar type of plot
dittoHeatmapOutputs a heatmap of given genes
dittoPlotPlots continuous data for cutomizable cells'/samples'...
dittoPlotVarsAcrossGroupsGenerates a dittoPlot where datapoints are genes/metadata...
dittoScatterPlotShow RNAseq data overlayed on a scatter plot
DittoSeqdittoSeq
geneReturns the values of a gene for all cells/samples
getGenesReturns the names of all genes of a target object.
getMetasReturns the names of all meta.data slots of a target object.
getReductionsReturns the names of all dimensionality reduction slots of a...
ImportDemux2SeuratExtracts Demuxlet information into a pre-made Seurat object
importDESeq2Creates an RNAseq object from a DESeq2 processed bulk RNAseq...
importEdgeRCreates an RNAseq object from edgeR or limma-voom processed...
isGeneTests if input is the name of a gene in a target object.
isMetaTests if an input is the name of a meta.data slot in a target...
LightenLightens input colors by a set amount
metaReturns the values of a meta.data for all cells/samples
meta.levelsGives the distinct values of a meta.data slot (or ident)
multi_dittoDimPlotGenerates multiple dittoDimPlots arranged in a grid.
multi_dittoDimPlotVaryCellsGenerates multiple dittoDimPlots, each showing different...
multi_dittoPlotGenerates multiple dittoPlots arranged into a grid.
RNAseq-classThe RNAseq Class
RNAseq_mockRNAseq_mock
SimulateSimulates what a colorblind person would see for any dittoSeq...
dtm2451/DittoSeq documentation built on Nov. 13, 2019, 8:22 a.m.