tests/testthat.R

In rnabioco/djvdj: A collection of single-cell V(D)J tools

library(testthat)
library(dplyr)
library(tidyr)
library(purrr)
library(tibble)
library(stringr)
library(SingleCellExperiment)
library(djvdj)
library(Seurat)

# Load GEX data
data_dir <- system.file("extdata/splen", package = "djvdj")

gex_dirs <- c(
  BL6 = file.path(data_dir, "BL6_GEX/filtered_feature_bc_matrix"),
  MD4 = file.path(data_dir, "MD4_GEX/filtered_feature_bc_matrix")
)

so <- gex_dirs |>
  Read10X() |>
  CreateSeuratObject() |>
  AddMetaData(splen_meta)

vdj_dirs <- c(
  BL6 = system.file("extdata/splen/BL6_BCR", package = "djvdj"),
  MD4 = system.file("extdata/splen/MD4_BCR", package = "djvdj")
)

test_so <- so |>
  import_vdj(vdj_dirs, define_clonotypes = "cdr3_gene")

test_check("djvdj")





# ### TESTING LARGE DATA ###
#
# # Generate test data
# n_reps <- 10
#
# vdj_dirs <- c(
#   BL6 = system.file("extdata/splen/BL6_BCR", package = "djvdj"),
#   MD4 = system.file("extdata/splen/MD4_BCR", package = "djvdj")
# )
#
# test_vdj <- splen_so |>
#   import_vdj(vdj_dirs, define_clonotypes = "cdr3_gene")
#
# test_vdj <- test_vdj@meta.data
#
# walk(seq_len(n_reps), ~ {
#   test_vdj <<- bind_rows(test_vdj, test_vdj)
# })
#
# test_vdj <- test_vdj %>%
#   mutate(clonotype_id = str_c(clonotype_id, row_number(clonotype_id) %% n_reps))