Package index

scRNA-seq

Functions for plotting single cell RNA-seq data

CellDimPlot()

Cell Dimension Reduction Plot

CellStatPlot()

Cell statistics plot

CellVelocityPlot()

Cell Velocity Plot

FeatureStatPlot()

Visualize feature expression and statistics across cell groups

ClustreePlot()

Visualize cluster stability across clustering resolutions

EnrichmentPlot()

Visualize gene set enrichment and over-representation analysis results

CCCPlot()

Visualize Cell-Cell Communication (CCC) Interactions

MarkersPlot()

Visualize differential expression markers

scTCR-seq/scBCR-seq

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

ClonalVolumePlot()

Clonal Volume Plot

ClonalAbundancePlot()

Clonal Abundance Plot

ClonalLengthPlot()

Clonal CDR3 Length Plot

ClonalResidencyPlot()

Clonal Residency Plot

ClonalCompositionPlot()

Clonal Composition Plot

ClonalOverlapPlot()

Clonal Overlap Plot

ClonalStatPlot()

Visualize clone abundance, frequency, and dynamics across groups

ClonalDiversityPlot()

Clonal Diversity Plot

ClonalGeneUsagePlot()

Visualize TCR/BCR gene segment usage

ClonalPositionalPlot()

Visualize positional properties of CDR3 sequences

ClonalKmerPlot()

Visualize CDR3 k-mer (motif) frequency

ClonalRarefactionPlot()

Clonal Rarefaction Plot

Spatial data visualization

Functions for plotting spatial data

SpatDimPlot()

Visualize categorical groups on spatial coordinates

SpatFeaturePlot()

Visualize feature expression on spatial coordinates

Visualizing using LLMs

Functions/Classes for visualizing using LLMs

SCPlotterChat

LLM-Powered Chat Interface for Single-Cell Visualization

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()

Programmatic clone selection for TCR/BCR repertoire analysis

Re-exports

Functions that are re-exported from plotthis

reexports GSEASummaryPlot GSEAPlot

Objects exported from other packages