Package index • scplotter

scRNA-seq

Functions for plotting single cell RNA-seq data

CellDimPlot(): Cell Dimension Reduction Plot

CellStatPlot(): Cell statistics plot

CellVelocityPlot(): Cell Velocity Plot

FeatureStatPlot(): Feature statistic plot

ClustreePlot(): Clustree plot

EnrichmentPlot(): Enrichment Plot

CCCPlot(): Cell-Cell Communication Plot

MarkersPlot(): Visualize Markers

scTCR-seq/scBCR-seq

Functions for plotting single cell TCR-seq/BCR-seq data

ClonalVolumePlot(): ClonalVolumePlot

ClonalAbundancePlot(): ClonalAbundancePlot

ClonalLengthPlot(): ClonalLengthPlot

ClonalResidencyPlot(): ClonalResidencyPlot

ClonalCompositionPlot(): ClonalCompositionPlot

ClonalOverlapPlot(): ClonalOverlapPlot

ClonalDynamicsPlot(): ClonalDynamicsPlot

ClonalStatPlot(): ClonalStatPlot

ClonalDiversityPlot(): ClonalDiversityPlot

ClonalGeneUsagePlot(): ClonalGeneUsagePlot

ClonalPositionalPlot(): ClonalPositionalPlot

ClonalKmerPlot(): ClonalKmerPlot

ClonalRarefactionPlot(): ClonalRarefactionPlot

Spatial data visualization

Functions for plotting spatial data

SpatDimPlot(): Plot categories for spatial data

SpatFeaturePlot(): Plot features for spatial data

Visualizing using LLMs

Functions/Classes for visualizing using LLMs

SCPlotterChat: SCPlotterChat Class

data

Built-in data sets

ifnb_sub: A subsetted version of 'ifnb' datasets

pancreas_sub: A subsetted version of mouse 'pancreas' datasets

cellphonedb_res: A toy example of CellPhoneDB output from LIANA

Clone selectors

Functions for selecting clones

top() sel() uniq() shared() gt() ge() lt() le() eq() ne() and() or(): Helper functions to select clones based on various criteria

Re-exports

Functions that are re-exported from plotthis

reexports GSEASummaryPlot GSEAPlot: Objects exported from other packages