Extract per-cell expression grouped for violin plots

Combines extract_gene_expression() with a grouping obs column and melts to long format, ready for stacked (one gene per row) violin plots.

Usage

extract_gene_violin_data(
  object,
  features,
  grouping_variable,
  scale = FALSE,
  clip = NULL,
  modality = c("rna", "adt"),
  layer = c("norm", "magic")
)

Arguments

object

A single cell class.

features

Character vector. Gene IDs to extract.

grouping_variable

String. Obs column to group by.

scale

Boolean. Whether to z-score the expression values.

clip

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

modality

String. One of c("rna", "adt").

layer

String. One of c("norm", "magic"), forwarded to extract_gene_expression().

Value

A long data.table with cell_id, group, gene and expression. gene is an ordered factor following features.

Examples

# long format expression grouped by cell type
sc <- demo_single_cells(prepped = FALSE)
head(extract_gene_violin_data(
  sc,
  features = get_gene_names(sc)[1:2],
  grouping_variable = "cell_grp"
))
#>     cell_id       group    gene expression
#>      <char>      <fctr>  <fctr>      <num>
#> 1: cell_001 cell_type_1 gene_01   6.222656
#> 2: cell_002 cell_type_2 gene_01   4.113281
#> 3: cell_003 cell_type_3 gene_01   4.300781
#> 4: cell_004 cell_type_1 gene_01   5.757812
#> 5: cell_005 cell_type_2 gene_01   0.000000
#> 6: cell_006 cell_type_3 gene_01   0.000000

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