scplotter

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

Installation

remotes::install_github("pwwang/scplotter")
# or
devtools::install_github("pwwang/scplotter")
# or using conda
$ conda install pwwang::r-scplotter

Credits

scplotter draws significant inspiration from the SCP package, which separates visualization from analysis and implements it in the plotthis package. Building on plotthis, scplotter offers advanced functions for visualizing single-cell sequencing data. Special thanks to the scRepertoire package for its APIs that facilitate the analysis of single-cell TCR/BCR sequencing data.

Gallery

scRNA-seq

CellDimPlot

CellStatPlot

ClustreePlot

FeatureStatPlot

EnrichmentPlot

GSEASummaryPlot | GSEAPlot

VolcanoPlot

CCCPlot (Cell-Cell Communication Plot)

scTCR-seq/scBCR-seq

ClonalVolumePlot | ClonalAbundancePlot | ClonalResidencyPlot | ClonalDynamicsPlot | ClonalCompositionPlot | ClonalOverlapPlot | ClonalGeneUsagePlot

ClonalRarefactionPlot | ClonalGeneUsagePlot | ClonalDiversityPlot | ClonalPositionalPlot

Visualization with LLMs

provider <- tidyprompt::llm_provider_openai(api_key = Sys.getenv("OPENAI_API_KEY"))
chat <- SCPlotterChat$new(provider = provider)
chat$ask("Generate a cell-cell communication plot for the cellphonedb_res data.")
# Tool identified:  CCCPlot
# Data object identified:  cellphonedb_res
# Running tool:  CCCPlot

chat$ask("Do a heatmap instead")
# Tool identified:  CCCPlot
# Data object identified:  cellphonedb_res
# Running tool:  CCCPlot