This function imports previously exported clustering results with cluster_export() and adds them to the colData() slot of your SpatialExperiment-class object.

cluster_import(
  spe,
  cluster_dir = file.path(tempdir(), "exported_clusters"),
  prefix = "imported_",
  overwrite = TRUE
)

Arguments

spe

Defaults to the output of fetch_data(type = 'spe'). This is a SpatialExperiment-class object with the spot-level Visium data and information required for visualizing the histology. See fetch_data() for more details.

cluster_dir

A character(1) specifying the output directory, similar to the outs/analysis/clustering produced by SpaceRanger.

prefix

A character(1) specifying the prefix to use when naming these new cluster variables.

overwrite

A logical(1) indicating whether to overwrite the spe$key.

Value

A SpatialExperiment-class object with the imported clusters appended on the colData().

See also

Other cluster export/import utility functions: cluster_export()

Examples

if (enough_ram()) {
    ## Obtain the necessary data
    if (!exists("spe")) spe <- fetch_data("spe")

    ## Export two cluster variables
    cluster_export(spe, "spatialLIBD")
    cluster_export(spe, "GraphBased")

    ## Re-import them
    colData(cluster_import(spe))
}
#> 2023-09-05 20:30:21.223666 loading file /github/home/.cache/R/BiocFileCache/152d33414640_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
#> Warning: '/tmp/RtmpD1p0FU/exported_clusters/spatialLIBD' already exists
#> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
#> Warning: '/tmp/RtmpD1p0FU/exported_clusters/GraphBased' already exists
#> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
#> DataFrame with 47681 rows and 71 columns
#>                                       key   sample_id   Cluster   sum_umi
#>                               <character> <character> <integer> <numeric>
#> AAACAACGAATAGTTC-1 AAACAACGAATAGTTC-1_1..      151507         6       948
#> AAACAAGTATCTCCCA-1 AAACAAGTATCTCCCA-1_1..      151507         3      4261
#> AAACAATCTACTAGCA-1 AAACAATCTACTAGCA-1_1..      151507         2      1969
#> AAACACCAATAACTGC-1 AAACACCAATAACTGC-1_1..      151507         5      3368
#> AAACAGCTTTCAGAAG-1 AAACAGCTTTCAGAAG-1_1..      151507         1      2981
#> ...                                   ...         ...       ...       ...
#> TTGTTGTGTGTCAAGA-1 TTGTTGTGTGTCAAGA-1_1..      151676         5      2880
#> TTGTTTCACATCCAGG-1 TTGTTTCACATCCAGG-1_1..      151676         2      2640
#> TTGTTTCATTAGTCTA-1 TTGTTTCATTAGTCTA-1_1..      151676         2      2063
#> TTGTTTCCATACAACT-1 TTGTTTCCATACAACT-1_1..      151676         7      1031
#> TTGTTTGTGTAAATTC-1 TTGTTTGTGTAAATTC-1_1..      151676         1      2625
#>                     sum_gene     subject    position   replicate
#>                    <integer> <character> <character> <character>
#> AAACAACGAATAGTTC-1       727      Br5292           0           1
#> AAACAAGTATCTCCCA-1      2170      Br5292           0           1
#> AAACAATCTACTAGCA-1      1093      Br5292           0           1
#> AAACACCAATAACTGC-1      1896      Br5292           0           1
#> AAACAGCTTTCAGAAG-1      1620      Br5292           0           1
#> ...                      ...         ...         ...         ...
#> TTGTTGTGTGTCAAGA-1      1638      Br8100         300           2
#> TTGTTTCACATCCAGG-1      1526      Br8100         300           2
#> TTGTTTCATTAGTCTA-1      1279      Br8100         300           2
#> TTGTTTCCATACAACT-1       748      Br8100         300           2
#> TTGTTTGTGTAAATTC-1      1392      Br8100         300           2
#>                    subject_position   discard cell_count SNN_k50_k4 SNN_k50_k5
#>                         <character> <logical>  <integer>  <integer>  <integer>
#> AAACAACGAATAGTTC-1      Br5292_pos0     FALSE          0          1          1
#> AAACAAGTATCTCCCA-1      Br5292_pos0     FALSE          3          1          1
#> AAACAATCTACTAGCA-1      Br5292_pos0     FALSE          2          3          2
#> AAACACCAATAACTGC-1      Br5292_pos0     FALSE          5          2          3
#> AAACAGCTTTCAGAAG-1      Br5292_pos0     FALSE          3          1          1
#> ...                             ...       ...        ...        ...        ...
#> TTGTTGTGTGTCAAGA-1    Br8100_pos300     FALSE          1          1          1
#> TTGTTTCACATCCAGG-1    Br8100_pos300     FALSE          6          2          3
#> TTGTTTCATTAGTCTA-1    Br8100_pos300     FALSE          9          2          3
#> TTGTTTCCATACAACT-1    Br8100_pos300     FALSE          2          1          1
#> TTGTTTGTGTAAATTC-1    Br8100_pos300     FALSE          0          1          1
#>                    SNN_k50_k6 SNN_k50_k7 SNN_k50_k8 SNN_k50_k9 SNN_k50_k10
#>                     <integer>  <integer>  <integer>  <integer>   <integer>
#> AAACAACGAATAGTTC-1          1          3          3          4           4
#> AAACAAGTATCTCCCA-1          1          1          1          1           1
#> AAACAATCTACTAGCA-1          3          4          4          5           5
#> AAACACCAATAACTGC-1          4          5          8          9          10
#> AAACAGCTTTCAGAAG-1          1          1          1          3           3
#> ...                       ...        ...        ...        ...         ...
#> TTGTTGTGTGTCAAGA-1          1          1          1          1           1
#> TTGTTTCACATCCAGG-1          4          5          6          7           8
#> TTGTTTCATTAGTCTA-1          4          5          6          7           8
#> TTGTTTCCATACAACT-1          1          1          1          3           3
#> TTGTTTGTGTAAATTC-1          2          2          2          2           2
#>                    SNN_k50_k11 SNN_k50_k12 SNN_k50_k13 SNN_k50_k14 SNN_k50_k15
#>                      <integer>   <integer>   <integer>   <integer>   <integer>
#> AAACAACGAATAGTTC-1           5           5           5           6           7
#> AAACAAGTATCTCCCA-1           4           4           4           4           3
#> AAACAATCTACTAGCA-1           6           6           6           7           8
#> AAACACCAATAACTGC-1          11          10           9          10          11
#> AAACAGCTTTCAGAAG-1           3           3           3           3           2
#> ...                        ...         ...         ...         ...         ...
#> TTGTTGTGTGTCAAGA-1           4           4           4           4           3
#> TTGTTTCACATCCAGG-1           9           8           8           9          10
#> TTGTTTCATTAGTCTA-1           9           8           8           9          10
#> TTGTTTCCATACAACT-1           3           3           3           3           2
#> TTGTTTGTGTAAATTC-1           1           1           1           1           5
#>                    SNN_k50_k16 SNN_k50_k17 SNN_k50_k18 SNN_k50_k19 SNN_k50_k20
#>                      <integer>   <integer>   <integer>   <integer>   <integer>
#> AAACAACGAATAGTTC-1           7           9          10          10          10
#> AAACAAGTATCTCCCA-1           3           3           2           2           2
#> AAACAATCTACTAGCA-1           8           7           8           8           8
#> AAACACCAATAACTGC-1          11          12          13          12          11
#> AAACAGCTTTCAGAAG-1           2           2           1           1           1
#> ...                        ...         ...         ...         ...         ...
#> TTGTTGTGTGTCAAGA-1           3           3           2           2           2
#> TTGTTTCACATCCAGG-1          10          11          12          18          18
#> TTGTTTCATTAGTCTA-1          10          11          12          15          15
#> TTGTTTCCATACAACT-1           2           2           1           1           1
#> TTGTTTGTGTAAATTC-1           5           5           5           5           5
#>                    SNN_k50_k21 SNN_k50_k22 SNN_k50_k23 SNN_k50_k24 SNN_k50_k25
#>                      <integer>   <integer>   <integer>   <integer>   <integer>
#> AAACAACGAATAGTTC-1          10          11          11          11          12
#> AAACAAGTATCTCCCA-1           2           1           1           1           6
#> AAACAATCTACTAGCA-1           8           9           9           9           9
#> AAACACCAATAACTGC-1          11          12          20          20          21
#> AAACAGCTTTCAGAAG-1           1           6           6           6           5
#> ...                        ...         ...         ...         ...         ...
#> TTGTTGTGTGTCAAGA-1           2           1           1           1          10
#> TTGTTTCACATCCAGG-1          17          18          17          17          18
#> TTGTTTCATTAGTCTA-1          14          15          14          13          14
#> TTGTTTCCATACAACT-1           1           6           6           6           5
#> TTGTTTGTGTAAATTC-1           5           4           4           4           3
#>                    SNN_k50_k26 SNN_k50_k27 SNN_k50_k28 GraphBased  Maynard
#>                      <integer>   <integer>   <integer>  <integer> <factor>
#> AAACAACGAATAGTTC-1          13          13          14          6       WM
#> AAACAAGTATCTCCCA-1           5           5           4          3       6 
#> AAACAATCTACTAGCA-1           9           9           9          2       1 
#> AAACACCAATAACTGC-1          22          21          22          5       5 
#> AAACAGCTTTCAGAAG-1           4           4           3          1       4 
#> ...                        ...         ...         ...        ...      ...
#> TTGTTGTGTGTCAAGA-1          10          10          10          5       5 
#> TTGTTTCACATCCAGG-1          19          18          19          2       WM
#> TTGTTTCATTAGTCTA-1          15          15          16          2       WM
#> TTGTTTCCATACAACT-1           4           4           3          7       6 
#> TTGTTTGTGTAAATTC-1           3           3           2          1       1 
#>                    Martinowich layer_guess layer_guess_reordered
#>                       <factor>    <factor>              <factor>
#> AAACAACGAATAGTTC-1          WM      Layer1                Layer1
#> AAACAAGTATCTCCCA-1          6       Layer3                Layer3
#> AAACAATCTACTAGCA-1          1       Layer1                Layer1
#> AAACACCAATAACTGC-1          5       WM                    WM    
#> AAACAGCTTTCAGAAG-1          4       Layer6                Layer6
#> ...                        ...         ...                   ...
#> TTGTTGTGTGTCAAGA-1          4       Layer6                Layer6
#> TTGTTTCACATCCAGG-1          WM      WM                    WM    
#> TTGTTTCATTAGTCTA-1          WM      WM                    WM    
#> TTGTTTCCATACAACT-1          6       Layer6                Layer6
#> TTGTTTGTGTAAATTC-1          1       Layer1                Layer1
#>                    layer_guess_reordered_short expr_chrM expr_chrM_ratio
#>                                       <factor> <numeric>       <numeric>
#> AAACAACGAATAGTTC-1                          L1        88       0.0928270
#> AAACAAGTATCTCCCA-1                          L3       657       0.1541892
#> AAACAATCTACTAGCA-1                          L1       431       0.2188928
#> AAACACCAATAACTGC-1                          WM       272       0.0807601
#> AAACAGCTTTCAGAAG-1                          L6       502       0.1683999
#> ...                                        ...       ...             ...
#> TTGTTGTGTGTCAAGA-1                          L6       475        0.164931
#> TTGTTTCACATCCAGG-1                          WM       320        0.121212
#> TTGTTTCATTAGTCTA-1                          WM       262        0.127000
#> TTGTTTCCATACAACT-1                          L6       161        0.156159
#> TTGTTTGTGTAAATTC-1                          L1       667        0.254095
#>                    SpatialDE_PCA SpatialDE_pool_PCA   HVG_PCA pseudobulk_PCA
#>                        <integer>          <integer> <integer>      <integer>
#> AAACAACGAATAGTTC-1             4                  5         3              5
#> AAACAAGTATCTCCCA-1             2                  3         1              2
#> AAACAATCTACTAGCA-1             4                  4         4              4
#> AAACACCAATAACTGC-1             6                  7         6              6
#> AAACAGCTTTCAGAAG-1             1                  1         3              1
#> ...                          ...                ...       ...            ...
#> TTGTTGTGTGTCAAGA-1             1                  2         2              2
#> TTGTTTCACATCCAGG-1             5                  5         4              5
#> TTGTTTCATTAGTCTA-1             5                  5         4              4
#> TTGTTTCCATACAACT-1             4                  8         6              2
#> TTGTTTGTGTAAATTC-1             1                  1         2              7
#>                    markers_PCA SpatialDE_UMAP SpatialDE_pool_UMAP  HVG_UMAP
#>                      <integer>      <integer>           <integer> <integer>
#> AAACAACGAATAGTTC-1           4              1                   2         1
#> AAACAAGTATCTCCCA-1           2              1                   3         1
#> AAACAATCTACTAGCA-1           8              2                   4         5
#> AAACACCAATAACTGC-1           8              5                   7         7
#> AAACAGCTTTCAGAAG-1           1              2                   3         6
#> ...                        ...            ...                 ...       ...
#> TTGTTGTGTGTCAAGA-1           1              1                   3         2
#> TTGTTTCACATCCAGG-1           6              4                   5         5
#> TTGTTTCATTAGTCTA-1           1              4                   5         7
#> TTGTTTCCATACAACT-1           3              1                   2         3
#> TTGTTTGTGTAAATTC-1           4              2                   1         4
#>                    pseudobulk_UMAP markers_UMAP SpatialDE_PCA_spatial
#>                          <integer>    <integer>             <integer>
#> AAACAACGAATAGTTC-1               3            1                     3
#> AAACAAGTATCTCCCA-1               2            1                     4
#> AAACAATCTACTAGCA-1               3            6                     3
#> AAACACCAATAACTGC-1               7            1                     7
#> AAACAGCTTTCAGAAG-1               1            1                     1
#> ...                            ...          ...                   ...
#> TTGTTGTGTGTCAAGA-1               2            3                     1
#> TTGTTTCACATCCAGG-1               6            1                     5
#> TTGTTTCATTAGTCTA-1               4            2                     5
#> TTGTTTCCATACAACT-1               3            1                     4
#> TTGTTTGTGTAAATTC-1               2            6                     2
#>                    SpatialDE_pool_PCA_spatial HVG_PCA_spatial
#>                                     <integer>       <integer>
#> AAACAACGAATAGTTC-1                          5               5
#> AAACAAGTATCTCCCA-1                          1               2
#> AAACAATCTACTAGCA-1                          4               3
#> AAACACCAATAACTGC-1                          6               7
#> AAACAGCTTTCAGAAG-1                          2               1
#> ...                                       ...             ...
#> TTGTTGTGTGTCAAGA-1                          1               4
#> TTGTTTCACATCCAGG-1                          5               5
#> TTGTTTCATTAGTCTA-1                          5               5
#> TTGTTTCCATACAACT-1                          8               2
#> TTGTTTGTGTAAATTC-1                          2               1
#>                    pseudobulk_PCA_spatial markers_PCA_spatial
#>                                 <integer>           <integer>
#> AAACAACGAATAGTTC-1                      4                   3
#> AAACAAGTATCTCCCA-1                      3                   1
#> AAACAATCTACTAGCA-1                      5                   7
#> AAACACCAATAACTGC-1                      7                   7
#> AAACAGCTTTCAGAAG-1                      1                   2
#> ...                                   ...                 ...
#> TTGTTGTGTGTCAAGA-1                      2                   6
#> TTGTTTCACATCCAGG-1                      4                   4
#> TTGTTTCATTAGTCTA-1                      4                   2
#> TTGTTTCCATACAACT-1                      2                   4
#> TTGTTTGTGTAAATTC-1                      3                   2
#>                    SpatialDE_UMAP_spatial SpatialDE_pool_UMAP_spatial
#>                                 <integer>                   <integer>
#> AAACAACGAATAGTTC-1                      1                           1
#> AAACAAGTATCTCCCA-1                      2                           2
#> AAACAATCTACTAGCA-1                      2                           1
#> AAACACCAATAACTGC-1                      7                           8
#> AAACAGCTTTCAGAAG-1                      8                           2
#> ...                                   ...                         ...
#> TTGTTGTGTGTCAAGA-1                      6                           1
#> TTGTTTCACATCCAGG-1                      5                           5
#> TTGTTTCATTAGTCTA-1                      5                           5
#> TTGTTTCCATACAACT-1                      2                           3
#> TTGTTTGTGTAAATTC-1                      1                           2
#>                    HVG_UMAP_spatial pseudobulk_UMAP_spatial
#>                           <integer>               <integer>
#> AAACAACGAATAGTTC-1                1                       1
#> AAACAAGTATCTCCCA-1                1                       2
#> AAACAATCTACTAGCA-1                4                       1
#> AAACACCAATAACTGC-1                7                       8
#> AAACAGCTTTCAGAAG-1                8                       1
#> ...                             ...                     ...
#> TTGTTGTGTGTCAAGA-1                4                       1
#> TTGTTTCACATCCAGG-1                5                       8
#> TTGTTTCATTAGTCTA-1                8                       1
#> TTGTTTCCATACAACT-1                2                       4
#> TTGTTTGTGTAAATTC-1                1                       2
#>                    markers_UMAP_spatial spatialLIBD ManualAnnotation in_tissue
#>                               <integer>    <factor>      <character> <logical>
#> AAACAACGAATAGTTC-1                    1          L1               NA      TRUE
#> AAACAAGTATCTCCCA-1                    1          L3               NA      TRUE
#> AAACAATCTACTAGCA-1                    6          L1               NA      TRUE
#> AAACACCAATAACTGC-1                    1          WM               NA      TRUE
#> AAACAGCTTTCAGAAG-1                    1          L6               NA      TRUE
#> ...                                 ...         ...              ...       ...
#> TTGTTGTGTGTCAAGA-1                    1          L6               NA      TRUE
#> TTGTTTCACATCCAGG-1                    1          WM               NA      TRUE
#> TTGTTTCATTAGTCTA-1                    1          WM               NA      TRUE
#> TTGTTTCCATACAACT-1                    7          L6               NA      TRUE
#> TTGTTTGTGTAAATTC-1                    5          L1               NA      TRUE
#>                    array_row array_col imported_GraphBased imported_spatialLIBD
#>                    <integer> <integer>           <integer>          <character>
#> AAACAACGAATAGTTC-1         0        16                   6                   L1
#> AAACAAGTATCTCCCA-1        50       102                   3                   L3
#> AAACAATCTACTAGCA-1         3        43                   2                   L1
#> AAACACCAATAACTGC-1        59        19                   5                   WM
#> AAACAGCTTTCAGAAG-1        43         9                   1                   L6
#> ...                      ...       ...                 ...                  ...
#> TTGTTGTGTGTCAAGA-1        31        77                   5                   L6
#> TTGTTTCACATCCAGG-1        58        42                   2                   WM
#> TTGTTTCATTAGTCTA-1        60        30                   2                   WM
#> TTGTTTCCATACAACT-1        45        27                   7                   L6
#> TTGTTTGTGTAAATTC-1         7        51                   1                   L1