'barcode' data for figure 2d of original simba paper

simba_barcode_data(
  symbols,
  origad,
  clabel,
  simbaref,
  cembpath,
  gembpath,
  layer = "softmax"
)

Arguments

symbols: character() vector of gene symbols for barcode visualization
origad: AnnData reference to original RNA-seq data
clabel: character(1) column name for entity type in origad
simbaref: instance of python module for simba
cembpath: character(1) path to h5ad file for cell embedding
gembpath: character(1) path to h5ad file for gene embedding
layer: character(1) either 'softmax' (default) or 'norm', used as source of scoring of strength of cell-gene association

Examples

sref = simba_ref()
p3k = sref$read_h5ad(get_10x3kpbmc_path(overwrite=TRUE))
myd = simba_barcode_data( symbols = c("MS4A1", "CST3", "NKG7"),
   origad = p3k, clabel = "celltype",
   simbaref = sref, cembpath = get_3k_cell_emb(),
   gembpath = get_3k_gene_emb() )
head(myd,3)
#>   rank       score attr symbol
#> 1    1 0.004509825    B  MS4A1
#> 2    2 0.003888108    B  MS4A1
#> 3    3 0.003783007    B  MS4A1
table(myd$symbol)
#> 
#>  CST3 MS4A1  NKG7 
#>  2700  2700  2700