ktplots

R plotting functions to plot gene expression data of single-cell data.

For a python port of ktplots, please check out my other repository.

Installation instructions

You can install the package via devtools::install_github() function in R

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
devtools::install_github('zktuong/ktplots', dependencies = TRUE)

Usage instructions

library(ktplots)

There is a test dataset in SingleCellExperiment format to test the functions.

library(SingleCellExperiment)
data(kidneyimmune)
#Some functions accept Seurat objects too.

The data is downsampled from the kidney cell atlas.

For more info, please see Stewart et al. kidney single cell data set published in Science 2019.

Vignette

Please go to the official vignette for more information.

For the legacy version of the README.md file, please go here.

Citation

If you find these functions useful, please consider leaving a star and cite this preprint:

Troulé K, Petryszak R, Prete M, Cranley J, Harasty A, Tuong ZK, Teichmann SA, Garcia-Alonso L, Vento-Tormo R. CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data. arXiv preprint arXiv:2311.04567. 2023 Nov 8.

Thank you!