R: 'FOV' Methods

FOV-methods {SeuratObject}

R Documentation

`FOV` Methods

Description

Methods for FOV objects

Usage

## S3 method for class 'FOV'
Cells(x, boundary = NULL, ...)

## S3 method for class 'FOV'
Features(x, set = NULL, ...)

## S3 method for class 'FOV'
FetchData(object, vars, cells = NULL, simplify = TRUE, ...)

## S3 method for class 'FOV'
GetTissueCoordinates(object, which = NULL, ...)

## S3 method for class 'FOV'
Keys(object, ...)

## S3 method for class 'FOV'
RenameCells(object, new.names = NULL, ...)

## S3 method for class 'FOV'
x$i, ...

## S3 method for class 'FOV'
x[i, j, ...]

## S3 method for class 'FOV'
x[[i, ...]]

## S3 method for class 'FOV'
length(x)

## S3 method for class 'FOV'
names(x)

## S3 method for class 'FOV'
subset(x, cells = NULL, features = NULL, ...)

## S4 replacement method for signature 'FOV,character,missing,Centroids'
x[[i, j, ...]] <- value

## S4 replacement method for signature 'FOV,character,missing,Molecules'
x[[i, j, ...]] <- value

## S4 replacement method for signature 'FOV,character,missing,'NULL''
x[[i, j, ...]] <- value

## S4 replacement method for signature 'FOV,character,missing,Segmentation'
x[[i, j, ...]] <- value

## S4 method for signature 'FOV'
show(object)

Arguments

`x, object`	A `FOV` object
`boundary, set`	Name of segmentation boundary or molecule set to extract cell or feature names for; pass `NA` to return all cells or feature names
`...`	Arguments passed to other methods
`vars`	A vector of variables to fetch; can be the name of a segmentation boundary, to get tissue coordinates, or molecule names, to get molecule coordinates
`simplify`	If only returning either boundary or molecule coordinates, return a single data frame instead of a list
`which`	Name of segmentation boundary or molecule set
`new.names`	vector of new cell names
`i, cells`	For `[[` and `[[<-`, the name of a segmentation or “molecules”; for `FetchData`, `subset`. and `[`, a vector of cells to keep
`j, features`	For `subset` and `[`, a vector of features to keep; for `[[<-`, not used
`value`	For `[[<-`, a replacement `Molecules`, `Centroids`, or `Segmentation` object; otherwise `NULL` to remove the boundary stored at `i`

Details

The following methods are defined for interacting with a FOV object:

Cells: Get cell names

Features: Get spatially-resolved molecule names

FetchData: Fetch boundary and/or molecule coordinates from a FOV object

GetTissueCoordinates: Get boundary or molecule coordinates from a FOV object

Keys: Get the keys of molecule sets contained within a FOV object

RenameCells: Update cell names

$, [[: Extract a segmentation boundary

length: Get the number of segmentation layers in a FOV object

names: Get the names of segmentation layers and molecule sets

subset, [: Subset a FOV object

[[<-: Add or remove segmentation layers and molecule information to/from a FOV object

show: Display an object summary to stdout

Value

Cells: A vector of cell names

Features: A vector of spatially-resolved molecule names; if no molecular information present, returns NULL

FetchData: If both molecule and boundary coordinates are requested, then a two-length list:

“molecules”: A data frame with the molecule coordinates requested. If molecules requested are keyed, the keys are preserved in the data frame
“coordinates”: A data frame with coordinates from the segmentation boundaries requested

If simplify is TRUE and only one data frame is generated, then only the data frame is returned. Otherwise, a one-length list is returned with the single data frame generated

GetTissueCoordinates: ...

Keys: A named vector of molecule set keys; names are the names of the molecule sets and values are the keys for the respective molecule set

RenameCells: object with the cells renamed to new.names

$, [[: The segmentation boundary or spatially-resolved molecule information stored at i

length: The number of segmentation layers (Segmentation or Centroids objects)

names: A vector of segmentation boundary and molecule set names

subset: x with just the cells and features specified

[[<-: Varies depending on the class of value:

If value is NULL, returns x with the boundary i removed; also allows removing molecules; does not allow removing the default segmentation
If value is a Molecules, returns x with value stored in molecules; requires that i is “molecules”
Otherwise, stores value as a segmentation boundary named i

show: Invisibly returns NULL