tests/testthat/test-scReplicate.R

In SydneyBioX/scMerge: scMerge: Merging multiple batches of scRNA-seq data

context("Test scReplicate")
data("example_sce", package = "scMerge")

set.seed(100)

## Error case:
expect_error(
    scReplicate(sce_combine = example_sce, 
                batch = example_sce$batch, 
                kmeansK = c(3, 3), 
                cell_type = example_sce$cellTypes, 
                cell_type_inc = 1:10, 
                cell_type_match = TRUE,
                verbose = TRUE))


## Case 1: supervised replicates: 
## Supply cell_type 
## Do not supply cell_type_inc 
## Do not upply cell_type_match
case1 = scReplicate(
    sce_combine = example_sce, 
    batch = example_sce$batch, 
    kmeansK = c(3, 3), 
    cell_type = example_sce$cellTypes, 
    cell_type_inc = NULL, 
    cell_type_match = FALSE,
    verbose = TRUE)

## Case 2.1: semi-supervised replicates version 2: 
## Supply cell_type 
## Do not supply cell_type_inc 
## Perform cell_type_match
## Do not supply marker 
## Do not supply marker_list
case2.1 = scReplicate(
    sce_combine = example_sce,
    batch = example_sce$batch,
    kmeansK = c(3, 3), 
    cell_type = example_sce$cellTypes, 
    cell_type_inc = NULL, 
    cell_type_match = TRUE, 
    marker = NULL, 
    marker_list = NULL,
    verbose = TRUE)


## Case 2.2: semi-supervised replicates version 2: 
## Supply cell_type 
## Do not supply cell_type_inc 
## Do not upply cell_type_match 
## Do not supply marker 
## Supply marker_list
case2.2 = scReplicate(
    sce_combine = example_sce, 
    batch = example_sce$batch,
    kmeansK = c(3, 3),
    cell_type = example_sce$cellTypes, 
    cell_type_inc = NULL, 
    cell_type_match = TRUE, 
    marker = NULL, 
    marker_list = 
        list(rownames(example_sce[1:10, ]), 
             rownames(example_sce[1:10, ])),
    verbose = TRUE)

## Case 2.3.1: semi-supervised replicates version 2: 
## Supply cell_type 
## Do not supply cell_type_inc 
## Do not supply cell_type_match
## Supply marker 
## Do not supply marker_list
case2.3.1 = scReplicate(
    sce_combine = example_sce, 
    batch = example_sce$batch, 
    kmeansK = c(3, 3), 
    cell_type = example_sce$cellTypes, 
    cell_type_inc = NULL, 
    cell_type_match = TRUE, 
    marker = rownames(example_sce[1:10, ]), 
    marker_list = NULL,
    verbose = TRUE)

## Case 2.3.2: semi-supervised replicates version 2: 
## Supply cell_type 
## Do not supply cell_type_inc 
## Do not upply cell_type_match 
## Supply marker 
## Supply marker_list
case2.3.2 = scReplicate(
    sce_combine = example_sce, 
    batch = example_sce$batch, 
    kmeansK = c(3, 3), 
    cell_type = example_sce$cellTypes, 
    cell_type_inc = NULL, 
    cell_type_match = TRUE, 
    marker = rownames(example_sce[1:10, ]),
    marker_list = 
        list(rownames(example_sce[1:10, ]), 
             rownames(example_sce[1:10, ])
        ),
    verbose = TRUE)

## Because case2.3.1 and 2.3.2 do not depend on the input of marker_list
## so their output should be identical
expect_identical(case2.3.1, case2.3.2)



## Semi-supervised version 1 in the vignette
case3 = scReplicate(
    sce_combine = example_sce, 
    batch = example_sce$batch, 
    kmeansK = c(3, 3), 
    cell_type = example_sce$cellTypes, 
    cell_type_inc = 1:10, 
    cell_type_match = FALSE,
    verbose = TRUE)

## Case 4.1: Do not Supply cell_type 
## Do not supply cell_type_inc 
## Do not supply cell_type_match 
## Do not supply marker 
## Do not supply marker_list
case4.1 = scReplicate(
    sce_combine = example_sce, 
    batch = example_sce$batch, 
    kmeansK = c(3, 3), 
    cell_type = NULL, 
    cell_type_inc = NULL, 
    cell_type_match = FALSE, 
    marker = NULL, 
    marker_list = NULL,
    verbose = TRUE)


## Case 4.2: 
## Do not supply cell_type 
## Do not supply cell_type_inc 
## Do not supply cell_type_match 
## Do not supply marker 
## Supply marker_list
case4.2 = scReplicate(
    sce_combine = example_sce,
    batch = example_sce$batch, 
    kmeansK = c(3, 3), 
    cell_type = NULL, 
    cell_type_inc = NULL, 
    cell_type_match = FALSE, 
    marker = NULL,
    marker_list = list(
        rownames(example_sce[1:10, ]), 
        rownames(example_sce[1:10, ])), 
    verbose = TRUE)

## Case 4.3: 
## Do not Supply cell_type 
## Do not supply cell_type_inc 
## Do not supply cell_type_match 
## Supply marker 
## Do not supply marker_list
case4.3 = scReplicate(
    sce_combine = example_sce, 
    batch = example_sce$batch, 
    kmeansK = c(3, 3), 
    cell_type = NULL, 
    cell_type_inc = NULL, 
    cell_type_match = FALSE, 
    marker = rownames(example_sce[1:10, ]), 
    marker_list = NULL,
    verbose = TRUE)



case4_WV1 = scReplicate(
    sce_combine = example_sce, 
    batch = example_sce$batch, 
    kmeansK = c(3, 3), 
    cell_type = NULL, 
    cell_type_inc = NULL, 
    cell_type_match = FALSE, 
    marker = NULL, 
    marker_list = NULL,
    WV = example_sce$cellTypes,
    verbose = TRUE)

case4_WV2 = scReplicate(
    sce_combine = example_sce, 
    batch = example_sce$batch, 
    kmeansK = c(3, 3), 
    cell_type = NULL, 
    cell_type_inc = NULL, 
    cell_type_match = FALSE, 
    marker = NULL, 
    marker_list = NULL,
    WV = example_sce$cellTypes,
    WV_marker = rownames(example_sce)[1:10],
    verbose = TRUE)