Create a PNAAssay object

Create a PNAAssay object from a count matrix and a list of CellGraph objects. The expected format of the input matrix is features x cells. Optionally, a tbl_df with proximity scores and a tbl_df with information on source PXL file paths can be provided.

Usage

CreatePNAAssay(
  counts,
  cellgraphs,
  proximity = NULL,
  fs_map = NULL,
  verbose = FALSE,
  ...
)

Arguments

counts

Unnormalized data (raw counts)

cellgraphs

A named list with CellGraph objects

proximity

A tbl_df with proximity scores

fs_map

A tbl_df with information on source PXL file paths, sample IDs, and component IDs

verbose

Print messages

...

Additional arguments passed to CreateAssayObject

Value

A PNAAssay object

Examples

library(pixelatorR)
library(dplyr)

pxl_file <- minimal_pna_pxl_file()
counts <- ReadPNA_counts(pxl_file)
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmp3BjCtL/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
pna_assay <- CreatePNAAssay(
  counts = counts,
  cellgraphs = rep(list(NULL), ncol(counts)) %>%
    setNames(colnames(counts))
)
pna_assay
#> PNAAssay data with 158 features for 5 cells
#> First 10 features:
#>  HLA-ABC, B2M, CD11b, CD11c, CD18, CD82, CD8, TCRab, HLA-DR, CD45 
#> Loaded CellGraph objects:
#>  0