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Create Multiplex Immunoflourescent object from a SpatialExperiment object

Source: R/spatial_exp_to_mif.R
spatial_exp_to_mif.Rd

Creates an MIF object for use in spatialIF functions using a Bioconductor SpatialExperiment object as input.

Usage

spatial_exp_to_mif(
  spatial_exp,
  markers,
  x_coord = "cell_x_position",
  y_coord = "cell_y_position",
  patient_id = "patient_id",
  sample_id = "sample_id",
  cols_to_keep = NULL,
  marker_pos_regex = "\\+"
)

Arguments

spatial_exp

A SpatialExperiment object to create a MIF from a SpatialExperiment Bioconductor object.

markers

A character vector that contains the name(s) of the columns that contains +/- for markers. This will be used to recode these columns into logical vectors for presence or absence of the marker. By default looks for a + to indicate presence. But this can be altered using the

x_coord

The name of the column in spatialCoords that contains the x coordinates for the cell. Default is "cell_x_position".

y_coord

The name of the column in spatialCoords that contains the y coordinates for the cell. Default is "cell_y_position".

patient_id

The name of the column in colData and metadata that contains the sample IDs. Default is "patient_id",

sample_id

The name of the column in colData and spatialCoords that contains the sample IDs. Default is "sample_id".

cols_to_keep

(Optional) By default only the patient_id, markers, sample_id, and x and y coordinate columns will be kept. But if there is additional information that needs to be kept, you can add those column names here. Or say "everything" if you want all columns to be kept. This may not be advisable for large datasets.

marker_pos_regex

By default will identify all markers columns as having a marker if a + is found in the data. But with this variable You can choose a different character to sort in presence/absence. Anything with the regex character given to this parameter will be labeled as positive and all other cells will be labeled as negative.

Value

Returns a custom MIF

clinical

Data frame of clinical data

sample

Data frame of sample data

spatial

Named list of spatial data

derived

List of data derived using the MIF object

patient_id

The column name for sample id in the sample data frame with the clinical data

sample_id

The column name for sample id in the sample data frame to merge with the spatial data

Author

Candace Savonen

Examples

# VectraPolarisData is a multi-gigabyte Bioconductor *data* package and is
# deliberately not a dependency of spatialTIME, so this example is not run.
# Install it once with BiocManager::install("VectraPolarisData") if you want to
# follow along; see vignette("spatialexperiment") for a worked version.
if (FALSE) { # \dontrun{
ovarian <- VectraPolarisData::HumanOvarianCancerVP()

ova_mif <- spatial_exp_to_mif(spatial_exp = ovarian, 
                              patient_id = "sample_id", 
                              markers = c("phenotype_cd68", "phenotype_cd3", "phenotype_cd8"))

spe_lung <- VectraPolarisData::HumanLungCancerV3()


spe_mif <- spatial_exp_to_mif(spatial_exp = spe_lung, 
                              patient_id = "slide_id", 
                              sample_id = "slide_id",
                              markers = c(
                                "phenotype_cd4", 
                                "phenotype_cd8", 
                                "phenotype_cd14", 
                                "phenotype_cd19", 
                                "phenotype_ck", 
                                "phenotype_other"))
} # }