join_features() extracts and joins information for specific features
Usage
# S4 method for Seurat
join_features(
.data,
features = NULL,
all = FALSE,
exclude_zeros = FALSE,
shape = "long",
assay = NULL,
slot = "data",
...
)Arguments
- .data
A tidyseurat object
- features
A vector of feature identifiers to join
- all
If TRUE return all
- exclude_zeros
If TRUE exclude zero values
- shape
Format of the returned table "long" or "wide"
- assay
assay name to extract feature abundance
- slot
slot name to extract feature abundance
- ...
Parameters to pass to join wide, i.e. assay name to extract feature abundance from and gene prefix, for shape="wide"
Details
This function extracts information for specified features and returns the information in either long or wide format.
Examples
data(pbmc_small)
pbmc_small %>% join_features(
features=c("HLA-DRA", "LYZ"))
#> tidyseurat says: This operation lead to duplicated cell names. A data frame is returned for independent data analysis.
#> # A tibble: 160 × 31
#> .cell .feature .abundance_RNA orig.ident nCount_RNA nFeature_RNA
#> <chr> <chr> <dbl> <fct> <dbl> <int>
#> 1 ATGCCAGAACGACT HLA-DRA 0 SeuratProject 70 47
#> 2 ATGCCAGAACGACT LYZ 4.97 SeuratProject 70 47
#> 3 CATGGCCTGTGCAT HLA-DRA 4.78 SeuratProject 85 52
#> 4 CATGGCCTGTGCAT LYZ 4.78 SeuratProject 85 52
#> 5 GAACCTGATGAACC HLA-DRA 0 SeuratProject 87 50
#> 6 GAACCTGATGAACC LYZ 4.75 SeuratProject 87 50
#> 7 TGACTGGATTCTCA HLA-DRA 0 SeuratProject 127 56
#> 8 TGACTGGATTCTCA LYZ 0 SeuratProject 127 56
#> 9 AGTCAGACTGCACA HLA-DRA 4.07 SeuratProject 173 53
#> 10 AGTCAGACTGCACA LYZ 0 SeuratProject 173 53
#> # ℹ 150 more rows
#> # ℹ 25 more variables: RNA_snn_res.0.8 <fct>, letter.idents <fct>,
#> # groups <chr>, RNA_snn_res.1 <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>