scplotter <a href="https://pwwang.github.io/scplotter/"><img src="man/figures/logo.png" align="right" height="139" alt="scplotter website" /></a>

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

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

Gallery

scRNA-seq

CellDimPlot

CellStatPlot

ClustreePlot | CellVelocityPlot

FeatureStatPlot

EnrichmentPlot

GSEASummaryPlot | GSEAPlot

MarkersPlot

CCCPlot (Cell-Cell Communication Plot)

scTCR-seq/scBCR-seq

Spatial data

SpatDimPlot | SpatFeaturePlot

Visualization with LLMs

r
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:  scplotter::cellphonedb_res
# Code ran:
# CCCPlot(cellphonedb_res, plot_type = "dot")

r
chat$ask("Do a heatmap instead")
# Tool identified:  CCCPlot
# Data object identified:  scplotter::cellphonedb_res
# Code ran:
# CCCPlot(cellphonedb_res, plot_type = "heatmap")

Documentation

Documentation can be found at: https://pwwang.github.io/scplotter/

Credits

scplotter is built upon the following fantastic packages:

plotthis for the core plotting functions.
tidyprompt for the LLM interface.
Seurat for the Seurat object support.
LIANA for the cell-cell communication analysis.
scRepertoire for the TCR/BCR repertoire analysis.
Giotto for the spatial data analysis.

Scplotter