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Create a SpatialExperiment object from data

convert_to_spe.Rd

convert_to_spe() Puts omics data (omics measurements, metadata and image(s) corresponding to samples' tissue) into a SpatialExperiment (SPE) object. Most spammR functions require the input data to be an SPE object.

Usage

convert_to_spe(
  dat,
  sample_meta,
  feature_meta,
  assay_name = "proteomics",
  sample_id = "sample",
  sample_colname = NULL,
  feature_meta_colname = NULL,
  spatial_coords_colnames = NULL,
  rescale_image = FALSE,
  image_files = NULL,
  image_ids = NULL,
  image_sample_ids = rep(sample_id, length(image_files))
)

Arguments

dat

Matrix or data frame with omics measurements. Rows are features, columns are samples

sample_meta

Data frame of metadata with either sample_colname or rownames as samples (if empty)

feature_meta

Data frame of metadata with either sample_colname or rownames as samples (if empty)

assay_name

Name to be given to the data in omics_measurements_file. Example: "abundance", "log2", "znormalized_log2" or any other descriptive name

sample_id

Name of sample, defaults to "sample01"

sample_colname

Column name in sample_meta table whose entries contain sample identifiers provided as column names in dat.

feature_meta_colname

Name of column in feature_meta, that is to be used for identifying features. If missing defaults to rownames, which should match rownames of dat

spatial_coords_colnames

A list containing names of columns in meta_dat that are spatial coordinates. Default value is NULL in which case no spatial coordinates are entered

rescale_image

A boolean set to true if you need to rescale image. Recommended when coordinates are pulled from metaspace and are known to fully cover the image

image_files

A list containing paths of image files to be stored in the SpatialExperiment object. More images can be added later, without using this function.

image_ids

A list containing image names/identifiers for image paths provided in image_files

image_sample_ids

A list of sample identifiers for each of the images provided in image_files, defaults to the value from sample_id

Value

spe.out a SpatialExperiment (SPE) object that contains all data and image(s). Ready to be used as input in spammR functions that require SPE object as input.

Examples


data(pancMeta)
data(protMeta)
data(smallPancData)
# We can put all samples into the same object (for statistical power)
pooledData <- dplyr::bind_cols(smallPancData)
pooled.panc.spe <- convert_to_spe(pooledData,
  pancMeta,
  protMeta,
  feature_meta_colname = "pancProts"
)
#> Spatial object created without spatial coordinate 
#>          column names provided. Distance based analysis will not be enabled.
#> Note: Only mapping metadata for 2986 features out of 3000 data points

# or we can add the inmage to a single data capture
img0.spe <- convert_to_spe(smallPancData$Image_0,
  pancMeta,
  protMeta,
  sample_id = "Image0",
  feature_meta_colname = "pancProts",
  image_files = system.file("extdata", "Image_0.png", package = "spammR"),
  spatial_coords_colnames = c("x_pixels", "y_pixels"),
  image_ids = "Image0"
)
#> Note: Only mapping metadata for 2986 features out of 3000 data points