/ktplots

Some tools for plotting single-cell data

Primary LanguageRMIT LicenseMIT

License: MIT codecov R DOI

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, citing this repository, and/or citing the following DOI:

To cite a specific version of ktplots, please follow the links on the zenodo repository. e.g. v2.0.0:

ZK Tuong. (2021). zktuong/ktplots: 2.0.0 (v2.0.0). Zenodo. https://doi.org/10.5281/zenodo.5717922

Thank you!