Bug when using joinFeatures + SingleCellExperiment with 1 cell

[multimeric]

There is some weird behaviour when using a SingleCellExperiment with one cell. Firstly, note that we have two .cell columns in the second example, and both of them become part of the full coldata:

This example works fine:

> tidySingleCellExperiment::pbmc_small[, 1:2] |> tidySingleCellExperiment::join_features("HLA-DRA")
# A SingleCellExperiment-tibble abstraction: 2 × 20
# Features=230 | Cells=2 | Assays=counts, logcounts
  .cell   .feat…¹ .abun…² .abun…³ orig.…⁴ nCoun…⁵ nFeat…⁶ RNA_s…⁷ lette…⁸ groups
  <chr>   <chr>     <dbl>   <dbl> <fct>     <dbl>   <int> <fct>   <fct>   <chr>
1 ATGCCA… HLA-DRA       0    0    Seurat…      70      47 0       A       g2
2 CATGGC… HLA-DRA       1    4.78 Seurat…      85      52 0       A       g1
# … with 10 more variables: RNA_snn_res.1 <fct>, file <chr>, ident <fct>,
#   PC_1 <dbl>, PC_2 <dbl>, PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, tSNE_1 <dbl>,
#   tSNE_2 <dbl>, and abbreviated variable names ¹.feature, ².abundance_counts,
#   ³.abundance_logcounts, ⁴orig.ident, ⁵nCount_RNA, ⁶nFeature_RNA,
#   ⁷RNA_snn_res.0.8, ⁸letter.idents
# ℹ Use `colnames()` to see all variable names

But as soon as we use one cell:

> tidySingleCellExperiment::pbmc_small[, 1] |> tidySingleCellExperiment::join_features("HLA-DRA")
New names:
• `.cell` -> `.cell...1`
• `.cell` -> `.cell...2`
tidySingleCellExperiment says: Key columns are missing. A data frame is returned for independent data analysis.
# A tibble: 1 × 35
  .feature .abundance_…¹ .abun…² .cell…³ .cell…⁴ orig.…⁵ nCoun…⁶ nFeat…⁷ RNA_s…⁸
  <chr>            <dbl>   <dbl> <chr>   <chr>   <fct>     <dbl>   <int> <fct>
1 HLA-DRA              0       0 .cell   ATGCCA… Seurat…      70      47 0
# … with 26 more variables: letter.idents <fct>, groups <chr>,
#   RNA_snn_res.1 <fct>, file <chr>, ident <fct>, PC_1 <dbl>, PC_2 <dbl>,
#   PC_3 <dbl>, PC_4 <dbl>, PC_5 <dbl>, PC_6 <dbl>, PC_7 <dbl>, PC_8 <dbl>,
#   PC_9 <dbl>, PC_10 <dbl>, PC_11 <dbl>, PC_12 <dbl>, PC_13 <dbl>,
#   PC_14 <dbl>, PC_15 <dbl>, PC_16 <dbl>, PC_17 <dbl>, PC_18 <dbl>,
#   PC_19 <dbl>, tSNE_1 <dbl>, tSNE_2 <dbl>, and abbreviated variable names
#   ¹.abundance_counts, ².abundance_logcounts, ³.cell...1, ⁴.cell...2, …
# ℹ Use `colnames()` to see all variable names
> tidySingleCellExperiment::pbmc_small[, 1] |> tidySingleCellExperiment::join_features("HLA-DRA") |> colnames()
New names:
• `.cell` -> `.cell...1`
• `.cell` -> `.cell...2`
tidySingleCellExperiment says: Key columns are missing. A data frame is returned for independent data analysis.
 [1] ".feature"             ".abundance_counts"    ".abundance_logcounts"
 [4] ".cell...1"            ".cell...2"            "orig.ident"
 [7] "nCount_RNA"           "nFeature_RNA"         "RNA_snn_res.0.8"
[10] "letter.idents"        "groups"               "RNA_snn_res.1"
[13] "file"                 "ident"                "PC_1"
[16] "PC_2"                 "PC_3"                 "PC_4"
[19] "PC_5"                 "PC_6"                 "PC_7"
[22] "PC_8"                 "PC_9"                 "PC_10"
[25] "PC_11"                "PC_12"                "PC_13"
[28] "PC_14"                "PC_15"                "PC_16"
[31] "PC_17"                "PC_18"                "PC_19"
[34] "tSNE_1"               "tSNE_2"

[stemangiola]

Thanks Michael. I will have a look.