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Extract a pair of features for scatter / hex plots

extract_feature_pair.Rd

Extracts two features into a wide data.table with feature_1 and feature_2 value columns, ready for a scatter or hex plot. Each feature may carry a _rna or _adt suffix to choose its modality independently (e.g. "ENSG00000167286_rna" against "CD3_adt"); features without a suffix fall back to modality. For SingleCells / MetaCells only RNA exists, so an _adt feature there errors via extract_gene_expression().

Usage

extract_feature_pair(
  object,
  feature_1,
  feature_2,
  obs_cols = NULL,
  scale = FALSE,
  clip = NULL,
  modality = c("rna", "adt"),
  layer = c("norm", "magic")
)

Arguments

object

A single cell class.

feature_1

String. First feature, optionally _rna / _adt suffixed.

feature_2

String. Second feature, optionally _rna / _adt suffixed.

obs_cols

Optional character vector. Obs columns to attach (e.g. to colour the scatter).

scale

Boolean. Whether to z-score the expression values per feature.

clip

Optional numeric. Clip z-scores if scale = TRUE.

modality

String. Fallback modality for unsuffixed features. One of c("rna", "adt").

layer

String. One of c("norm", "magic"), forwarded to extract_gene_expression(). Applies to both features, and an _adt suffixed one will error under "magic".

Value

A data.table with cell_id, feature_1, feature_2 and any requested obs columns. The original feature labels are stored in a features attribute as c(feature_1, feature_2).

Examples

# two genes side by side, ready for a scatter
sc <- demo_single_cells(prepped = FALSE)
genes <- get_gene_names(sc)[1:2]
head(extract_feature_pair(sc, genes[1], genes[2], obs_cols = "cell_grp"))
#> Key: <cell_id>
#>     cell_id feature_1 feature_2    cell_grp
#>      <char>     <num>     <num>      <char>
#> 1: cell_001  6.222656  6.761719 cell_type_1
#> 2: cell_002  4.113281  4.511719 cell_type_2
#> 3: cell_003  4.300781  4.300781 cell_type_3
#> 4: cell_004  5.757812  5.757812 cell_type_1
#> 5: cell_005  0.000000  0.000000 cell_type_2
#> 6: cell_006  0.000000  4.234375 cell_type_3

unlink(sc@dir_data, recursive = TRUE, force = TRUE)