tests/testthat/test-citeseq.R

In bimberlabinternal/OOSAP: OHSU-ONPRC Single-cell Analysis Package

context("scRNAseq")

# test_that("Cite-Seq works", {
  # #Reduce size, touch up data:
  # seuratObj <- readRDS('../testdata/seuratOutput.rds')
	# seuratObj <- seuratObj[1:1000,1:100]
	#
	# #this is technically cell hashing, but shouldnt matter:
	# countDir <- '../testdata/cellHashing/umi_count'
	# citeseqData <- Seurat::Read10X(data.dir = countDir, gene.column=1, strip.suffix = TRUE)
	# citeseqData1 <- citeseqData[,1:40]
	# colnames(citeseqData1) <- colnames(seuratObj)[1:40]
	# inputPath1 <- './input1'
	# if (dir.exists(inputPath1)) {
	#   unlink(inputPath1, recursive = T)
	# }
	# DropletUtils::write10xCounts(inputPath1, citeseqData1)
	#
	# citeseqData2 <- citeseqData[,60:100]
	# colnames(citeseqData2) <- colnames(seuratObj)[60:100]
	# inputPath2 <- './input2'
	# if (dir.exists(inputPath2)) {
	#   unlink(inputPath2, recursive = T)
	# }
	# DropletUtils::write10xCounts(inputPath2, citeseqData2)
	#
	# citeseqData3 <- citeseqData[,60:100]
	# colnames(citeseqData3) <- colnames(seuratObj)[60:100]
	# rownames(citeseqData3) <- c('NewMarkerName', 'unmapped')
	# inputPath3 <- './input3'
	# if (dir.exists(inputPath3)) {
	#   unlink(inputPath3, recursive = T)
	# }
	# DropletUtils::write10xCounts(inputPath3, citeseqData3)
	#
	# #First w/o prefix:
	# seuratObjCite <- OOSAP:::AppendCiteSeq(seuratObj = seuratObj, countMatrixDir = inputPath1, barcodePrefix = NULL)
	# expect_equal(colnames(seuratObjCite@assays$ADT), colnames(seuratObj@assays$RNA))
	# expect_equal(rownames(seuratObjCite@assays$ADT), rownames(citeseqData1)[rownames(citeseqData1) != 'unmapped'])
  # data <- Seurat::GetAssayData(seuratObjCite, assay = 'ADT', slot = 'counts')
  # expect_equal(max(data[,41:100]), 0) #These have no data
  # expect_equal(max(data[,1:40]), 6)
	#
	# #Rename cells with a barcodeprefix:
	# seuratObj@meta.data$BarcodePrefix <- c(rep('12345', 50), rep('67890', 50))
	# seuratObj <- Seurat::RenameCells(object = seuratObj, new.names = paste0(seuratObj@meta.data$BarcodePrefix, '_', colnames(seuratObj)))
	#
	# #With prefix, no assay present
	# seuratObjCite <- OOSAP:::AppendCiteSeq(seuratObj = seuratObj, countMatrixDir = inputPath1, barcodePrefix = '12345')
	# expect_equal(colnames(seuratObjCite@assays$ADT), colnames(seuratObj@assays$RNA))
	# expect_equal(rownames(seuratObjCite@assays$ADT), rownames(citeseqData1)[rownames(citeseqData1) != 'unmapped'])
	# data <- Seurat::GetAssayData(seuratObjCite, assay = 'ADT', slot = 'counts')
	# expect_equal(max(data[,41:100]), 0) #These have no data
	# expect_equal(max(data[,1:40]), 6)
	#
	# OOSAP:::.PlotCiteSeqCountData(seuratObj = seuratObjCite, assayName = 'ADT')
	#
	# #Now add again, existing assay present:
	# seuratObjCite2 <- OOSAP:::AppendCiteSeq(seuratObj = seuratObjCite, countMatrixDir = inputPath2, barcodePrefix = '67890', minRowSum = 0)
	# d1 <- Seurat::GetAssayData(seuratObjCite, 'ADT', slot = 'counts')
	# d2 <- Seurat::GetAssayData(seuratObjCite2, 'ADT', slot = 'counts')
	# expect_equal(d2[,1:50], d1[,1:50]) #The original data
	# expect_equal(max(d2[,41:59]), 0) #These have no data
	# expect_equal(max(d2[,60:100]), 1)
	#
	# #This time with: differing sets of features:
	# seuratObjCite3 <- OOSAP:::AppendCiteSeq(seuratObj = seuratObjCite, countMatrixDir = inputPath3, barcodePrefix = '67890', minRowSum = 0)
	# d1 <- Seurat::GetAssayData(seuratObjCite, 'ADT', slot = 'counts')
	# d2 <- Seurat::GetAssayData(seuratObjCite3, 'ADT', slot = 'counts')
	# expect_equal(nrow(d2), 2) #our new marker is added
	# expect_equal(d2[1,1:50], d1[1,1:50]) #The original data
	# values <- rep(0, 50)
	# names(values) <- colnames(d2)[1:50]
	# expect_equal(d2[2,1:50], values) #Blank appended data
	# expect_equal(max(d2[,41:59]), 0) #These have no data
	# expect_equal(max(d2[,60:100]), 1)
	#
	# #Test feature metadata add:
	# metafile <- 'citeseqMeta.txt'
	# meta <- data.frame(tagname = c('HTO-8'), sequence = c('CTCCTCTGCAATTAC'), markername = c('RenamedField'), otherfield = c('Value1'))
	# write.table(meta, file = metafile, sep = '\t', row.names = F)
	#
	# seuratObjCiteMeta <- OOSAP:::AppendCiteSeq(seuratObj = seuratObj, countMatrixDir = inputPath1, barcodePrefix = '12345', featureLabelTable = metafile)
	# expect_equal(colnames(seuratObjCiteMeta@assays$ADT), colnames(seuratObj@assays$RNA))
	# expect_equal(rownames(seuratObjCiteMeta@assays$ADT), c('RenamedField'))
	# data <- Seurat::GetAssayData(seuratObjCiteMeta, assay = 'ADT', slot = 'counts')
	# expect_equal(Seurat::GetAssay(seuratObjCiteMeta, assay = 'ADT')@meta.features$otherfield, c('Value1'))
	# expect_equal(max(data[,41:100]), 0) #These have no data
	# expect_equal(max(data[,1:40]), 6)
	#
	# unlink(inputPath1, recursive = T)
	# unlink(inputPath2, recursive = T)
	# unlink(inputPath3, recursive = T)
	# unlink(metafile)
# })