Extra functions

2024-10-31

First, ensure you have the devtools R package installed, which allows you to install packages from GitHub. If devtools is installed, you can easily install viewmastR using the following command:

devtools::install_github("furlan-lab/viewmastR")

# Load required packages
suppressPackageStartupMessages({
  library(viewmastR)
  library(Seurat)
  library(ggplot2)
  library(scCustomize)
  library(httpgd)
})


# Load query and reference datasets
seu <- readRDS(file.path(ROOT_DIR1, "240813_final_object.RDS"))

A clean Seurat object

DimPlot(seu, group.by = "ground_truth")

Exporting R objects to scanpy is painful… As an inefficient but effective work around we have written code that enables you to export a Seurat object to the same three file format output by cellranger. This makes import into scanpy a breeze.

The command creates a folder called 3file in the directory you provide. By default the meta data, reductions, and variable features are exported.

Currently, only Seurat objects are supported

make3file(seu, dir = file.path(ROOT_DIR1))
list.files(file.path(ROOT_DIR1, "3file"))

## [1] "barcodes.tsv.gz"         "features.tsv.gz"        
## [3] "matrix.mtx.gz"           "meta.csv"               
## [5] "pca_reduction.tsv.gz"    "umap_reduction.tsv.gz"  
## [7] "variablefeatures.tsv.gz"