Read an MPX data item

ReadMPX_item reads any number of items from a PXL file. If multiple items are specified, the output is a list of tbl_df objects. Otherwise the output is a single tbl_df. ReadMPX_polarization, ReadMPX_colocalization and ReadMPX_edgelist are wrappers for ReadMPX_item to read specific items.

Usage

ReadMPX_item(
  filename,
  items = c("colocalization", "polarization", "edgelist"),
  verbose = TRUE
)

ReadMPX_polarization(filename, verbose = TRUE)

ReadMPX_colocalization(filename, verbose = TRUE)

ReadMPX_edgelist(filename, verbose = TRUE)

Arguments

filename

Path to a PXL file

items

One or several of "colocalization", "polarization", "edgelist"

verbose

Print messages

Value

Either an object of class tbl_df or a list of tbl_df objects if multiple items are selected

See also

Other data-loaders: ReadMPX_Seurat(), ReadPNA_proximity()

Examples

library(pixelatorR)

# Load example data
pxl_file <- minimal_mpx_pxl_file()
polarization <- ReadMPX_item(pxl_file, items = "polarization")
#> ℹ Loading item(s) from: /private/var/folders/gw/bdcqhnvs0m9gs_mq8n51jtbc0000gn/T/Rtmp9yI9aG/temp_libpath1491327224194/pixelatorR/extdata/five_cells/five_cells.pxl
#> →   Loading polarization data
#> ✔ Returning a 'tbl_df' object
polarization
#> # A tibble: 380 × 6
#>    morans_i morans_p_value morans_p_adjusted morans_z marker component    
#>       <dbl>          <dbl>             <dbl>    <dbl> <chr>  <chr>        
#>  1 -0.00165          0.894             0.999   -0.134 ACTB   RCVCMP0000217
#>  2 -0.00734          0.499             0.999   -0.676 B2M    RCVCMP0000217
#>  3 -0.00850          0.409             0.999   -0.826 CD102  RCVCMP0000217
#>  4  0.00102          0.856             0.999    0.182 CD11a  RCVCMP0000217
#>  5 -0.00381          0.656             0.999   -0.445 CD11b  RCVCMP0000217
#>  6 -0.00493          0.631             0.999   -0.480 CD11c  RCVCMP0000217
#>  7 -0.00497          0.596             0.999   -0.530 CD127  RCVCMP0000217
#>  8 -0.00150          0.910             0.999   -0.113 CD137  RCVCMP0000217
#>  9 -0.00224          0.850             0.999   -0.190 CD14   RCVCMP0000217
#> 10 -0.00246          0.837             0.999   -0.205 CD150  RCVCMP0000217
#> # ℹ 370 more rows

# Alternative 2
polarization <- ReadMPX_polarization(pxl_file)
#> ℹ Loading item(s) from: /private/var/folders/gw/bdcqhnvs0m9gs_mq8n51jtbc0000gn/T/Rtmp9yI9aG/temp_libpath1491327224194/pixelatorR/extdata/five_cells/five_cells.pxl
#> →   Loading polarization data
#> ✔ Returning a 'tbl_df' object