Retrieve data objects from metaspace

retrieve_metaspace_dataCollects data from http://metaspace2020.org by project id and returns it in SpatialExperiment object

Usage

retrieve_metaspace_data(
  project_id = "2024-02-15_20h37m13s",
  fdr = 0.2,
  assay_name = "lipids",
  sample_id = "sample",
  rotate = FALSE,
  drop_zeroes = TRUE,
  y_offset = 0,
  x_offset = 0
)

Arguments

project_id

Identifier for project

fdr

FDR value above which to collect data

assay_name

Name of assay to include in object

sample_id

Name of sample

rotate

Set to TRUE if x and y coordinates need to be swapped

drop_zeroes

Set to TRUE to drop zeroes and set the values to NAs. If False the zeroes will be included in the image data.

y_offset

Number of pixels to adjust y based on image

x_offset

Number of pixels to adjust x based on image

Value

a SpatialExperiment object with the metaspace data and coordinates.

Details

This relies on underlying python code and environment to run, including the metaspace2020 package, the numpy package, and the pandas package.

Examples

# \donttest{
rdat <- retrieve_metaspace_data(project_id = "2024-02-15_20h37m13s",
                                fdr = 0.2,
                                assay_name = 'lipids',
                               sample_id = 'sample')
#> Downloading ion data from metaspace...
#> Warning: index contains duplicated values: row names not set
head(rowMeans(assay(rdat,'lipids')))
#> C46H78NO10P-H-  C47H83O13P-H-    C20H32O2-H-    C22H32O2-H-    C16H30O2-H- 
#>             NA             NA             NA             NA             NA 
#> C42H80NO10P-H- 
#>             NA 
# }