Code for generating data, figures used in the SCUBA manuscript

To run the code in the Rmd files included in this repo, SCUBA and all dependencies must be installed. For more information, see the "Pre-requisites" and "Installation" sections of the SCUBA repo README.

Data

The objects used for demonstration in the SCUBA manuscript exists in the SCUBA repo and can be accessed by calling library(SCUBA) and then running one of the three functions below.

The objects were derived from the Accute Myeloid Leukemia (AML) reference dataset created by Triana et al. 2021. Demo_Object_Generation.Rmd contains all code needed to generate each of the three objects from the inital dataset.

# Seurat Object
AML_Seurat

# SingleCellExperiment Object
AML_SCE()

# anndata object
AML_h5ad()

Contents

• Demo_Object_Generation.Rmd: code for generating the AML_Seurat, AML_SCE(), and AML_h5ad() datasets from the Triana et al. 2021 reference dataset.
• Fig2.Rmd: examples of FetchData methods added by SCUBA for SingleCellExperiment and anndata objects alongside the existing Seurat method, as shown in Figure 2 of the manuscript.
• Fig3.Rmd: examples of fetch_metadata and fetch_reduction generics created by SCUBA for the retrieval of metadata and reductions, repsectively.
• Fig4.Rmd: code used to evaluate performance of FetchData on a large multimodal reference dataset.
• Fig5.Rmd: code demonstrating the use of SCUBA methods as a foundation for plotting.
• Fig6.Rmd: example usage of SCUBA to view the unique values of a metadata variable in an object, a common object exploration operation.