Package 'VoltRon'

Title: VoltRon for Spatial Omics Data Integration and Analysis
Description: VoltRon is a spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is capable of analyzing multiple types and modalities of spatially-aware datasets. VoltRon visualizes and analyzes regions of interests (ROIs), spots, cells, molecules and event tiles.
Authors: Artür Manukyan, Ella Bahry, Raj Prateek Rai, Wei-Che Ko, Markus Landthaler, Altuna Akalin
Maintainer: Artür Manukyan <[email protected]>
License: MIT + file LICENSE
Version: 0.2.6
Built: 2026-05-22 10:01:07 UTC
Source: https://github.com/BIMSBbioinfo/VoltRon

Help Index

VoltRon: VoltRon for Spatial Omics Data Integration and Analysis

Description

VoltRon is a spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is capable of analyzing multiple types and modalities of spatially-aware datasets. VoltRon visualizes and analyzes regions of interests (ROIs), spots, cells, molecules and event tiles.

Add Assay

Description

add a new assay (vrAssay object) to a VoltRon object

Usage

addAssay(object, ...)

## S4 method for signature 'vrMetadata'
addAssay(
  object,
  metadata = NULL,
  assay,
  assay_name,
  sample = "Sample1",
  layer = "Section1"
)

## S4 method for signature 'VoltRon'
addAssay(
  object,
  assay,
  metadata = NULL,
  assay_name,
  sample = "Sample1",
  layer = "Section1"
)

Arguments

object

a VoltRon object.
...

arguments passed to other methods.
metadata

a predefined metadata
assay

a vrAssay object
assay_name

assay name of the new added assay
sample

sample name
layer

layer name

addBlockConnectivity

Description

add connectivity information to the layers (vrLayer) of the same block (Block)

Usage

addBlockConnectivity(object, connectivity, zlocation = NULL, sample)

Arguments

object

a VoltRon object
connectivity

a metadata of edges representing connected layers within a block
zlocation

zlocation
sample

sample name

addFeature

Description

add a new feature set to a vrAssay (or VoltRon) object

Usage

addFeature(object, ...)

## S4 method for signature 'vrAssayV2'
addFeature(object, data, feature_name)

## S4 method for signature 'VoltRon'
addFeature(object, assay = NULL, data, feature_name)

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
data

new data matrix for new feature set
feature_name

the name of the new feature set
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. If NULL, the default assay will be used, see vrMainAssay. If given as "all", then provides a summary of spatial systems across all assays.

addMetadata

Description

adding new columns or updating the values of the existing columns

Usage

addMetadata(object, assay = NULL, type = NULL, value, label)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
type

the assay type: ROI, spot or cell, or all for the entire metadata object
value

the new values of the metadata column
label

the label of the new column, either a new column or an existing one

addSpatialLayer

Description

adding additional layers of spatial plots to an existing vrSpatialPlot.

Usage

addSpatialLayer(
  g,
  object,
  assay,
  group.by = "Sample",
  plot.segments = FALSE,
  group.ids = NULL,
  reg = FALSE,
  colors = NULL,
  alpha = 1,
  n.tile = NULL,
  pt.size = 2,
  cell.shape = 21,
  graph = NULL,
  graph.edge.color = "orange",
  spatial = NULL,
  combine.groups = FALSE
)

Arguments

g

ggplot object
object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
group.by

a column of metadata from Metadata used as grouping label for the spatial entities
plot.segments

plot segments from vrSegments instead of points
group.ids

a subset of categories defined in metadata column from group.by
reg

TRUE if registered coordinates of the main image (vrMainSpatial) is requested
colors

the color set for group.by. Should be of the same size of group.id (if specified) or unique elements in group.by
alpha

alpha level of colors of visualized points and segments
n.tile

The number of tiles on x-and y-axis for rasterizing points (see geom_tile). The rasterization is performed automatically for large number of points Only applicable to spots, cells and molecules. If n.tile = 0 will turn of automated rasterization.
pt.size

point size
cell.shape

the shape of the points representing cells, see geom_point
graph

if not NULL, the graph is added to the plot
graph.edge.color

the color of graph edges, if graph is not NULL.
spatial

the name of the main spatial system
combine.groups

if TRUE, tile colors will reflect relative abundance of either of two groups, strictly for visualizing two groups when assay is a molecule typed and tiled (see n.tile).

annotateSpatialData

Description

A mini shiny app to for annotating spatial points

Usage

annotateSpatialData(
  object,
  label = "annotation",
  assay = NULL,
  annotation_assay = "ROIAnnotation",
  use.image.only = FALSE,
  shiny.options = list(launch.browser = getOption("shiny.launch.browser", interactive())),
  image_name = NULL,
  channel = NULL,
  ...
)

Arguments

object

a VoltRon object
label

the name of the new metadata column (default: annotation) annotating spatial points by selected polygons
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
annotation_assay

name of the annotation assay ()
use.image.only

if TRUE, use only the image
shiny.options

a list of shiny options (launch.browser, host, port etc.) passed options arguement of shinyApp. For more information, see runApp
image_name

the name/key of the image
channel

the name of the main channel
...

additional parameters passed to vrSpatialPlot.

Examples

## Not run: 
# Annotate based on images
visium_data <- annotateSpatialData(visium_data, use.image.only = TRUE)

# Annotate based on spatial plot
xenium_data <- annotateSpatialData(xenium_data, group.by = "clusters")

## End(Not run)

as.AnnData

Description

Converting a VoltRon object into a AnnData (.h5ad) object

Usage

as.AnnData(
  object,
  file,
  assay = NULL,
  flip_coordinates = FALSE,
  method = "anndata",
  create.ometiff = FALSE,
  python.path = NULL,
  ...
)

Arguments

object

a VoltRon object
file

the name of the h5ad file.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
flip_coordinates

if TRUE, the spatial coordinates (including segments) will be flipped.
method

the package to use for conversion: "anndataR" or "anndata".
create.ometiff

should an ometiff file be generated of default image of the object
python.path

the path to the python binary, otherwise either basilisk package is used or getOption("voltron.python.path") should be not NULL.
...

additional parameters passed to vrImages.

Details

This function converts a VoltRon object into an AnnData object (.h5ad file). It extracts assay data, spatial coordinates, and optionally flips coordinates. Images associated with the assay can be included in the resulting AnnData file, with additional customization parameters like channel, scale.perc.

as.Giotto

Description

Converting a VoltRon object into a Giotto object

Usage

as.Giotto(object, assay = NULL, reg = FALSE)

Arguments

object

a VoltRon object
assay

the name of the assay to be converted
reg

if TRUE, registered coordinates will be used

as.OmeTiff

Description

Converting VoltRon (magick) images to ome.tiff

Usage

as.OmeTiff(object, out_path, image_id = "image_1", python.path = NULL)

Arguments

object

a magick-image object
out_path

output path to ome.tiff file
image_id

image name
python.path

the path to the python binary, otherwise either basilisk package is used or getOption("voltron.python.path") should be not NULL.

as.OmeZarr

Description

Converting VoltRon (magick) images to ome.tiff

Usage

as.OmeZarr(object, out_path, image_id = "image_1")

Arguments

object

a magick-image object
out_path

output path to ome.tiff file
image_id

image name

as.Seurat

Description

Converting a VoltRon object into a Seurat object

Usage

as.Seurat(
  object,
  cell.assay = NULL,
  molecule.assay = NULL,
  image_key = "fov",
  type = c("image", "spatial"),
  reg = FALSE
)

Arguments

object

a VoltRon object
cell.assay

the name(type) of the cell assay to be converted
molecule.assay

the name(type) of the molecule assay to be added to the cell assay in Seurat object
image_key

the name (or prefix) of the image(s)
type

the spatial data type of Seurat object: "image" or "spatial"
reg

if TRUE, registered coordinates will be used

as.SpatialExperiment

Description

Converting a VoltRon object into a SpatialExperiment object

Usage

as.SpatialExperiment(object, assay = NULL, reg = FALSE)

Arguments

object

a VoltRon object
assay

the name of the assay to be converted
reg

if TRUE, registered coordinates will be used

as.VoltRon

Description

Generic methods for conversion into a VoltRon object

Usage

as.VoltRon(object, ...)

## S3 method for class 'Seurat'
as.VoltRon(
  object,
  type = c("image", "spatial"),
  assay_name = NULL,
  verbose = TRUE,
  ...
)

## S3 method for class 'SpatialExperiment'
as.VoltRon(
  object,
  assay_type = "cell",
  assay_name = NULL,
  image_id = NULL,
  verbose = TRUE,
  ...
)

Arguments

object

a Seurat or SpatialExperiment object
...

Additional parameter passed to formVoltRon
type

the spatial data type of Seurat object: "image" or "spatial"
assay_name

the assay name of the voltron assays (e.g. Visium, Xenium etc.)
verbose

verbose
assay_type

one of two types, 'cell' or 'spot' etc.
image_id

select image_id names if needed.

as.Zarr

Description

Generic methods to save VoltRon or magick-image objects as zarr files

Usage

as.Zarr(object, out_path, image_id)

## S3 method for class ''magick-image''
as.Zarr(object, out_path, image_id = "image_1")

Arguments

object

a VoltRon or magick-image object
out_path

output path to zarr file
image_id

image name

combineChannels

Description

Combining channels into novel channels of the same image

Usage

combineChannels(object, ...)

## S4 method for signature 'VoltRon'
combineChannels(
  object,
  assay = NULL,
  name = NULL,
  reg = FALSE,
  channels = NULL,
  colors = NULL,
  channel_key = "combined"
)

## S4 method for signature 'vrAssay'
combineChannels(
  object,
  name = NULL,
  reg = FALSE,
  channels = NULL,
  colors = NULL,
  channel_key = "combined"
)

## S4 method for signature 'vrAssayV2'
combineChannels(
  object,
  name = NULL,
  reg = FALSE,
  channels = NULL,
  colors = NULL,
  channel_key = "combined"
)

## S4 method for signature 'vrImage'
combineChannels(
  object,
  channels = NULL,
  colors = NULL,
  channel_key = "combined"
)

## S4 method for signature 'vrSpatial'
combineChannels(
  object,
  channels = NULL,
  colors = NULL,
  channel_key = "combined"
)

Arguments

object

a VoltRon, vrAssay or vrSpatial object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
name

the name of the image
reg

TRUE if registered coordinates of the main image (vrMainSpatial) is requested
channels

the name of the channel associated with the image
colors

the colors associated with each channel
channel_key

the name of the new channel name

combineGraphs

Description

Combining the edges of multiple graphs

Usage

combineGraphs(
  object,
  graph.names = NULL,
  graph.weights = NULL,
  graph.key = "combined"
)

Arguments

object

a VoltRon Object
graph.names

a vector of graph names
graph.weights

the weights for edges of each graph.
graph.key

the name of the combined graph

convertAnnDataToVoltRon

Description

converting AnnData h5ad files to VoltRon objects

Usage

convertAnnDataToVoltRon(file, AssayID = NULL, ...)

Arguments

file

h5ad file
AssayID

the ID assays in the h5ad file
...

additional parameters passed to formVoltRon

demuxVoltRon

Description

Subsetting/demultiplexing of the VoltRon Object using interactive shiny app

Usage

demuxVoltRon(
  object,
  max.pixel.size = 1200,
  use.points.only = FALSE,
  shiny.options = list(launch.browser = getOption("shiny.launch.browser", interactive()))
)

Arguments

object

a VoltRon object
max.pixel.size

the initial width of the object image
use.points.only

use spatial points instead of the reference image
shiny.options

a list of shiny options (launch.browser, host, port etc.) passed options arguement of shinyApp. For more information, see runApp

Fast creation of dummy variables

Description

Quickly create dummy (binary) columns from character and factor type columns in the inputted data (and numeric columns if specified.) This function is useful for statistical analysis when you want binary columns rather than character columns. Adapted from the fastDummies package (https://jacobkap.github.io/fastDummies/)

Usage

dummy_cols(
  .data,
  select_columns = NULL,
  remove_first_dummy = FALSE,
  remove_most_frequent_dummy = FALSE,
  ignore_na = FALSE,
  split = NULL,
  remove_selected_columns = FALSE,
  omit_colname_prefix = FALSE
)

Arguments

.data

An object with the data set you want to make dummy columns from.
select_columns

Vector of column names that you want to create dummy variables from. If NULL (default), uses all character and factor columns.
remove_first_dummy

Removes the first dummy of every variable such that only n-1 dummies remain. This avoids multicollinearity issues in models.
remove_most_frequent_dummy

Removes the most frequently observed category such that only n-1 dummies remain. If there is a tie for most frequent, will remove the first (by alphabetical order) category that is tied for most frequent.
ignore_na

If TRUE, ignores any NA values in the column. If FALSE (default), then it will make a dummy column for value_NA and give a 1 in any row which has a NA value.
split

A string to split a column when multiple categories are in the cell. For example, if a variable is Pets and the rows are "cat", "dog", and "turtle", each of these pets would become its own dummy column. If one row is "cat, dog", then a split value of "," this row would have a value of 1 for both the cat and dog dummy columns.
remove_selected_columns

If TRUE (not default), removes the columns used to generate the dummy columns.
omit_colname_prefix

If TRUE (not default) and 'length(select_columns) == 1', omit pre-pending the name of 'select_columns' to the names of the newly generated dummy columns

Value

A data.frame (or tibble or data.table, depending on input data type) with same number of rows as inputted data and original columns plus the newly created dummy columns.

fixVoltRon

Description

fixVoltRon

Usage

fixVoltRon(object)

Arguments

object

a VoltRon object

flipCoordinates

Description

Flip the coordinates of spatial points in the y axis direction.

Usage

flipCoordinates(object, ...)

## S4 method for signature 'VoltRon'
flipCoordinates(
  object,
  assay = NULL,
  image_name = NULL,
  spatial_name = NULL,
  ...
)

## S4 method for signature 'vrAssay'
flipCoordinates(object, image_name = NULL, spatial_name = NULL, ...)

## S4 method for signature 'vrAssayV2'
flipCoordinates(object, image_name = NULL, spatial_name = NULL, ...)

Arguments

object

a VoltRon, vrAssay or vrSpatial object.
...

additional parameters passed to vrCoordinates and vrSegments
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
image_name

(deprecated, use spatial_name) the name/key of the image
spatial_name

the name/key of the spatial system associated with the coordinates

formAssay

Description

Create a vrAssay (VoltRon assay) object

Usage

formAssay(
  data = NULL,
  coords,
  segments = list(),
  image = NULL,
  params = list(),
  type = "ROI",
  name = "Assay1",
  main_image = "image_1",
  main_featureset = NULL,
  assay_version = "v2",
  ...
)

Arguments

data

the feature matrix of spatialpoints
coords

the coordinates of the spatial points
segments

the list of segments each associated with a spatial point (optional)
image

a singelton or list of images as magick-image objects
params

additional parameters of the object
type

the type of the assay (tile, molecule, cell, spot or ROI)
name

the name of the assay
main_image

the name of the main_image
main_featureset

the name of the main_featureset
assay_version

the assay version
...

additional arguements passed to formImage

formImage

Description

Create a vrImage (VoltRon image) object

Usage

formImage(coords, segments = list(), image = NULL, main_channel = NULL)

Arguments

coords

the coordinates of the spatial points
segments

the list of segments each associated with a spatial point
image

a singelton or list of images as magick-image objects
main_channel

the key of the main channel of vrImage object

formVoltRon

Description

Create a VoltRon object

Usage

formVoltRon(
  data = NULL,
  metadata = NULL,
  image = NULL,
  coords,
  segments = list(),
  sample.metadata = NULL,
  main.assay = NULL,
  assay.type = "cell",
  params = list(),
  sample_name = NULL,
  layer_name = NULL,
  image_name = NULL,
  feature_name = NULL,
  project = NULL,
  version = "v2",
  ...
)

Arguments

data

the feature matrix of spatialpoints
metadata

a metadata object of class vrMetadata
image

a singelton or list of images as magick-image objects
coords

the coordinates of the spatial points
segments

the list of segments each associated with a spatial point
sample.metadata

a data frame of the sample metadata, see SampleMetadata
main.assay

the name of the main assay
assay.type

the type of the assay (tile, molecule, cell, spot or ROI)
params

additional parameters
sample_name

the name of the sample
layer_name

the name of the layer
image_name

the name/key of the image
feature_name

the name/key of the feature set
project

project name
version

the assay version, V1 or V2
...

additional parameters passed to formAssay

FromSegmentToCrop

Description

get magick crop information from coordinates of a segment

Usage

FromSegmentToCrop(segment, imageinfo)

Arguments

segment

coordinates of a segment
imageinfo

info of the image

generateCosMxImage

Description

Generates a low resolution Morphology image of the CosMx experiment

Usage

generateCosMxImage(
  dir.path,
  fov.position.file,
  increase.contrast = FALSE,
  output.path = NULL,
  verbose = TRUE,
  ...
)

Arguments

dir.path

CosMx folder of images
fov.position.file

the file providing FOV positions
increase.contrast

increase the contrast of the image before writing
output.path

The path to the new morphology image created if the image should be saved to a location other than Xenium output folder.
verbose

verbose
...

additional parameters passed to the writeImage function

generateGeoJSON

Description

Generating geojson files from segments

Usage

generateGeoJSON(segments, file)

Arguments

segments

the segments, typically from vrSegments.
file

the GeoJSON file, typically to be used by QuPath software.

generateSegments

Description

The function to import segments from a geojson file

Usage

generateSegments(geojson.file)

Arguments

geojson.file

the GeoJSON file, typically generated by QuPath software

generateTileData

Description

Generating data matrices for tile-based VoltRon objects from images

Usage

generateTileData(object, ...)

## S4 method for signature 'VoltRon'
generateTileData(object, assay = NULL, ...)

## S4 method for signature 'vrAssay'
generateTileData(object, name = NULL, reg = FALSE, channel = NULL)

## S4 method for signature 'vrAssayV2'
generateTileData(object, name = NULL, reg = FALSE, channel = NULL)

Arguments

object

a VoltRon or vrAssay object.
...

additional parameters passed to vrAssay.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
name

the name of the main spatial system
reg

TRUE if registered coordinates of the main image (vrMainSpatial) is requested
channel

the name of the channel associated with the image

generateXeniumImage

Description

Generate a low resolution DAPI image of the Xenium experiment

Usage

generateXeniumImage(
  dir.path,
  increase.contrast = TRUE,
  resolution_level = 7,
  overwrite_resolution = FALSE,
  output.path = NULL,
  file.name = "morphology_lowres.tif",
  verbose = TRUE,
  ...
)

Arguments

dir.path

Xenium output folder
increase.contrast

increase the contrast of the image before writing
resolution_level

the level of resolution within Xenium OME-TIFF image. Default: 7 (553x402)
overwrite_resolution

if TRUE, the image "file.name" will be generated again although it exists at "dir.path"
output.path

The path to the new morphology image created if the image should be saved to a location other than Xenium output folder.
file.name

the name of the lowred morphology image. Default: morphology_lowres.tif
verbose

verbose
...

additional parameters passed to the writeImage function

Details

The Xenium morphology_mip.ome.tif file that is found under the outs folder comes is an hyperstack of different resolutions of the DAPI image. generateXeniumImage allows extracting only one of these layers by specifying the resolution parameter (Default: 7 for 553x402) among 1 to 8. Lower incides of resolutions have higher higher resolutions, e.g. 1 for 35416x25778. Note that you may need to allocate larger memory of Java to import higher resolution images.

get the Python Basilisk environment

Description

Defines a conda environment via Basilisk, which is used to convert R objects to Zarr stores.

Usage

getBasilisk()

getClusters

Description

Get clustering of the VoltRon object

Usage

getClusters(
  object,
  assay = NULL,
  label = "clusters",
  method = "leiden",
  resolution = 1,
  graph = "kNN",
  data.type = "norm",
  dims = 1:30,
  nclus = integer(0),
  distance_measure = "euclidean",
  abundance_limit = 2,
  seed = 1
)

Arguments

object

a VoltRon object.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
label

the name for the newly created clustering column in the metadata.
method

The method of clustering. Use : (i) 'leiden' to perform graph clustering and (ii) 'kmeans' for K-means based clustering (iii) 'hierarchical' for hierarchical clustering.
resolution

the resolution parameter for leiden clustering.
graph

the graph type to be used.
data.type

the type of data used to cluster spatial points: "norm" (default), "raw" or an existing embeddings vrEmbeddingNames.
dims

the number of dimensions extracted from the embedding if data.type is not NULL
nclus

The number of cluster centers for K-means or hierarchical clustering.
distance_measure

the distance measure used by hierarchical clustering. See method for a list of distance measures in dist.
abundance_limit

the minimum number of points for a cluster, hence clusters with abundance lower than this limit will be appointed to other nearby clusters.
seed

seed.

getDeconvolution

Description

Calculate deconvolution of spots and ROIs

Usage

getDeconvolution(
  object,
  assay = NULL,
  features = NULL,
  sc.object,
  sc.assay = "RNA",
  sc.cluster = "seurat_clusters",
  method = "RCTD",
  ...
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
features

features
sc.object

Seurat Object
sc.assay

assay of the Seurat Object used for the single cell data reference
sc.cluster

metadata column variable used for the single cell data reference
method

Deconvolution method, RCTD (spot), SPOTlight (spot), MuSiC (ROI)
...

additional parameters passed to method specific functions, e.g. RCTD, MuSiC.

getDiffExp

Description

Get differential expression with DESeq2

Usage

getDiffExp(
  object,
  assay = NULL,
  group.by,
  group.base = NULL,
  covariates = NULL,
  method = "DESeq2"
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
group.by

the categorical variable from metadata to get differentially expressed features across
group.base

Optional, the base category in group.by which is used as control group
covariates

the covariate variable for the design formula
method

the method for DE analysis, e.g. DESeq2

getFeatures

Description

Get variable features of assays

Usage

getFeatures(object, ...)

## S4 method for signature 'VoltRon'
getFeatures(object, assay = NULL, max.count = 1, n = 3000)

## S4 method for signature 'vrAssay'
getFeatures(object, max.count = 1, n = 3000)

## S4 method for signature 'vrAssayV2'
getFeatures(object, max.count = 1, n = 3000)

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
max.count

maximum count (across spatial points) for low count filtering
n

the top number of variable features

getHotSpotAnalysis

Description

Conduct hot spot detection

Usage

getHotSpotAnalysis(
  object,
  assay = NULL,
  method = "Getis-Ord",
  features,
  graph.type = NULL,
  group.ids = NULL,
  alpha.value = 0.01,
  norm = TRUE,
  n.tile = 0,
  verbose = TRUE
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
method

the statistical method of conducting hot spot analysis. Default is "Getis-Ord"
features

a set of features to be visualized, either from vrFeatures of raw or normalized data or columns of the Metadata.
graph.type

the type of graph to determine spatial neighborhood
group.ids

a subset of categories defined in metadata column from features, throws an error if the feature does not include
alpha.value

the alpha value for the hot spot analysis test. Default is 0.01
norm

if TRUE, the normalized data is used
n.tile

should points be rasterized along x-and y-axes, typically used for molecule assays to generate features for Getis-Ord statistics
verbose

verbose

getNicheAssay

Description

Create Niche Assays

Usage

getNicheAssay(
  object,
  assay = NULL,
  label = NULL,
  graph.type = "delaunay",
  new_feature_name = "Niche"
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
label

grouping label for Niche definition
graph.type

the type of graph to determine spatial neighborhood
new_feature_name

the name of the new feature set created for the niche assay. Default: "Niche"

getOmeTiffChannels

Description

Function that returns the channel names of an image in a ome.tiff file

Usage

getOmeTiffChannels(ome.tiff)

Arguments

ome.tiff

location to ome.tiff file

getPCA

Description

calculate PCA of the VoltRon objects

Usage

getPCA(
  object,
  assay = NULL,
  features = NULL,
  feat_type = NULL,
  data.type = "norm",
  dims = 30,
  pca.key = "pca",
  n.workers = 1,
  overwrite = FALSE,
  seed = 1
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
features

the selected features for PCA reduction
feat_type

the feature set type
data.type

the type of data used to calculate PCA from: "norm" (default), "raw" or an existing embeddings vrEmbeddingNames.
dims

the number of dimensions extracted from PCA
pca.key

the key name for the embedding, default: pca
n.workers

the number of cores/workers use for parallelization.
overwrite

Whether the existing embedding with name 'type' should be overwritten in vrEmbeddings
seed

seed

Get profile specific neighbors

Description

Get neighbors of spatial points

Usage

getProfileNeighbors(
  object,
  assay = NULL,
  method = "kNN",
  k = 10,
  data.type = "pca",
  dims = seq_len(30),
  graph.key = method
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
method

the method used for graph construction, SNN or kNN
k

number of neighbors for kNN
data.type

the type of embedding used for neighborhood calculation, e.g. raw counts (raw), normalized counts (norm), PCA embeddings (pca), UMAP embeddings (umap) etc.
dims

the set of dimensions of the embedding data
graph.key

the name of the graph

getRcppAutomatedRegistration

Description

Automated registration workflos with Rcpp

Usage

getRcppAutomatedRegistration(
  ref_image,
  query_image,
  GOOD_MATCH_PERCENT = 0.15,
  MAX_FEATURES = 500,
  invert_query = FALSE,
  invert_ref = FALSE,
  flipflop_query = "None",
  flipflop_ref = "None",
  rotate_query = "0",
  rotate_ref = "0",
  matcher = "FLANN",
  method = "Homography",
  nonrigid = "TPS (OpenCV)"
)

Arguments

ref_image

reference image
query_image

query image
GOOD_MATCH_PERCENT

the percentage of good matching keypoints, used by "Brute force" method
MAX_FEATURES

maximum number of detected features, i.e. keypoints, used by "Brute force" method
invert_query

invert query image?
invert_ref

invert reference image
flipflop_query

flip or flop the query image
flipflop_ref

flip or flop the reference image
rotate_query

rotation of query image
rotate_ref

rotation of reference image
matcher

the matching method for landmarks/keypoints FLANN or BRUTE-FORCE
method

the automated registration method, Homography or Homography+TPS
nonrigid

the non-rigid registration method, "TPS (OpenCV)" or "BSpline (SimpleITK)"

getRcppManualRegistration

Description

Manual registration workflow with Rcpp

Usage

getRcppManualRegistration(
  query_image,
  ref_image,
  query_landmark,
  reference_landmark,
  method = "Homography",
  nonrigid = "TPS (OpenCV)"
)

Arguments

query_image

query image
ref_image

reference image
query_landmark

query landmark points
reference_landmark

refernece landmark points
method

the automated registration method, either TPS or Homography+TPS
nonrigid

the non-rigid registration method, "TPS (OpenCV)" or "BSpline (SimpleITK)"

Get spatial neighbors

Description

get neighbors in an assay given spatial coordinates

Usage

getSpatialNeighbors(
  object,
  assay = NULL,
  group.by = NULL,
  group.ids = NULL,
  method = "delaunay",
  k = 10,
  radius = numeric(0),
  graph.key = method,
  calculate.distances = FALSE,
  verbose = TRUE
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
group.by

a column of metadata from Metadata used as grouping label for the spatial entities.
group.ids

a subset of categories defined in metadata column from group.by.
method

the method spatial connectivity: "delaunay", "spatialkNN", "radius".
k

number of neighbors for kNN.
radius

When method = "radius" selected, determines the radius of a neighborhood ball around each spatial point.
graph.key

the name of the graph.
calculate.distances

If TRUE, distances between neighbors are also stored in the graph.
verbose

verbose

getUMAP

Description

calculate UMAP of the VoltRon objects

Usage

getUMAP(
  object,
  assay = NULL,
  data.type = "pca",
  dims = seq_len(30),
  umap.key = "umap",
  overwrite = FALSE,
  seed = 1
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
data.type

the type of data used to calculate UMAP from: "pca" (default), "raw" or "norm"
dims

the number of dimensions extracted from PCA
umap.key

the name of the umap embedding, default: umap
overwrite

Whether the existing embedding with name 'type' should be overwritten in vrEmbeddings
seed

seed

getVariableFeatures

Description

get shared variable features across multiple assays

Usage

getVariableFeatures(object, assay = NULL, n = 3000, ...)

Arguments

object

a VoltRon Object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
n

the number of features
...

additional arguements passed to vrFeatureData

import10Xh5

Description

import the sparse matrix from the H5 file

Usage

import10Xh5(filename)

Arguments

filename

the path to h5 file

importCosMx

Description

Import CosMx data

Usage

importCosMx(
  path,
  assay_name = "CosMx",
  image = NULL,
  image_name = "main",
  import_molecules = FALSE,
  verbose = TRUE,
  method = "CSV",
  feature_name = NULL,
  ...
)

Arguments

path

the path to the tiledb folder
assay_name

the assay name, default: CosMx
image

the reference morphology image of the CosMx assay
image_name

the image name of the CosMx assay, Default: main
import_molecules

if TRUE, molecule assay will be created along with cell assay.
verbose

verbose
method

the approach for importing the CosMx assay either by the folder of CSVs or with TileDB array.
feature_name

the name/key of the feature set.
...

additional parameters passed to formVoltRon

importDBITSeq

Description

Importing DBIT-Seq data

Usage

importDBITSeq(
  path.rna,
  path.prot = NULL,
  size = 10,
  assay_name = "DBIT-Seq",
  sample_name = NULL,
  image_name = "main",
  channel_name = "H&E",
  ...
)

Arguments

path.rna

path to rna count matrix
path.prot

path to protein count matrix
size

the size of the in situ pixel (defualt is 10 (micron))
assay_name

the assay name
sample_name

the name of the sample
image_name

the image name of the Visium assay, Default: main
channel_name

the channel name of the image of the Visium assay, Default: H&E
...

additional parameters passed to formVoltRon

importGenePS

Description

Importing GenePS data

Usage

importGenePS(
  dir.path,
  assay_name = "GenePS",
  sample_name = NULL,
  use_image = TRUE,
  resolution_level = 7,
  image_name = "main",
  channel_name = "DAPI",
  import_molecules = FALSE,
  verbose = TRUE,
  ...
)

Arguments

dir.path

path to Xenium output folder
assay_name

the assay name of the SR object
sample_name

the name of the sample
use_image

if TRUE, the DAPI image will be used.
resolution_level

the level of resolution within TIFF image. Default: 7 (971x638)
image_name

the image name of the Xenium assay, Default: main
channel_name

the channel name of the image of the Xenium assay, Default: DAPI
import_molecules

if TRUE, molecule assay will be created along with cell assay.
verbose

verbose
...

additional parameters passed to formVoltRon

importGeoMx

Description

Import GeoMx data

Usage

importGeoMx(
  dcc.path,
  pkc.file,
  summarySegment,
  summarySegmentSheetName,
  assay_name = "GeoMx",
  image = NULL,
  segment_polygons = FALSE,
  ome.tiff = NULL,
  resolution_level = 3,
  image_name = "main",
  verbose = TRUE,
  ...
)

Arguments

dcc.path

path to the folder where the dcc files are found
pkc.file

path to the pkc file
summarySegment

the metadata csv (sep = ";") or excel file, if the file is an excel file, summarySegmentSheetName should be provided as well.
summarySegmentSheetName

the sheet name of the excel file, summarySegment
assay_name

the assay name, default: GeoMx
image

the reference morphology image of the GeoMx assay
segment_polygons

if TRUE, the ROI polygons are parsed from the OME.TIFF file
ome.tiff

the OME.TIFF file of the GeoMx experiment if exists
resolution_level

the level of resolution within GeoMx OME-TIFF image, Default: 3
image_name

the image name of the Visium assay, Default: main
verbose

verbose
...

additional parameters passed to formVoltRon

importImageData

Description

import an image as VoltRon object

Usage

importImageData(
  image,
  tile.size = 10,
  segments = NULL,
  image_name = "main",
  channels = NULL,
  series = 1,
  resolution = NULL,
  is.RGB = TRUE,
  ...
)

Arguments

image

a single or a list of image paths or magick-image objects
tile.size

the size of tiles
segments

Either a list of segments or a GeoJSON file. This will result in a second assay in the VoltRon object to be created
image_name

the image name of the Image assay, Default: main
channels

the channel names of the images if multiple images are provided
series

the series IDs of the pyramidal image, typical an integer starting from 1
resolution

the resolution IDs of the pyramidal image, typical an integer starting from 1
is.RGB

If TRUE, all three channel images will be converted to RGB images.
...

additional parameters passed to formVoltRon

Examples

# single image
imgfile <- system.file("extdata", "DAPI.tif", package = "VoltRon")
vrdata <- importImageData(imgfile, image_name = "main")

# multiple images
imgfile <- c(system.file("extdata", "DAPI.tif", package = "VoltRon"),
             system.file("extdata", "DAPI.tif", package = "VoltRon"))
vrdata <- importImageData(imgfile, image_name = "main",
                                   channels = c("DAPI", "DAPI2"))

importOpenST

Description

Importing OpenST data

Usage

importOpenST(
  h5ad.path,
  assay_name = "OpenST",
  sample_name = NULL,
  image_name = "main",
  channel_name = "H&E",
  verbose = TRUE,
  ...
)

Arguments

h5ad.path

path to h5ad file of STOmics output
assay_name

the assay name
sample_name

the name of the sample
image_name

the image name of the Visium assay, Default: main
channel_name

the channel name of the image of the Visium assay, Default: H&E
verbose

verbose
...

additional parameters passed to formVoltRon

importPhenoCycler

Description

Importing PhenoCycler data

Usage

importPhenoCycler(
  dir.path,
  assay_name = "PhenoCycler",
  sample_name = NULL,
  image_name = "main",
  type = c("inform", "processor", "qupath"),
  filter = "DAPI|Blank|Empty",
  inform.quant = c("mean", "total", "min", "max", "std"),
  verbose = TRUE,
  ...
)

Arguments

dir.path

path to PhenoCycler output folder
assay_name

the assay name of the SR object
sample_name

the name of the sample
image_name

the image name of the Xenium assay, Default: main
type

Specify which type matrix is being provided.

  • “processor”: matrix generated by CODEX Processor

  • “inform”: matrix generated by inForm

  • “qupath”: matrix generated by QuPath

filter

A pattern to filter features by; pass NA to skip feature filtering
inform.quant

When type is “inform”, the quantification level to read in
verbose

verbose
...

additional parameters passed to formVoltRon

importImageData

Description

import an QuPath-quantified IF assay as VoltRon object

Usage

importQuPathIF(
  measurements,
  image,
  segments,
  image_name = "main",
  channels = NULL,
  series = 1,
  resolution = NULL,
  ...
)

Arguments

measurements

measurements
image

a single or a list of image paths or magick-image objects
segments

Either a list of segments or a GeoJSON file. This will result in a second assay in the VoltRon object to be created
image_name

the image name of the Image assay, Default: main
channels

the channel names of the images if multiple images are provided
series

the series IDs of the pyramidal image, typically an integer starting from 1
resolution

the resolution IDs of the pyramidal image, typically an integer starting from 1
...

additional parameters passed to formVoltRon

importSTOmics

Description

Importing STOmics (Stereo-Seq) data

Usage

importSTOmics(
  h5ad.path,
  assay_name = "STOmics",
  sample_name = NULL,
  image_name = "main",
  channel_name = "H&E",
  ...
)

Arguments

h5ad.path

path to h5ad file of STOmics output
assay_name

the assay name
sample_name

the name of the sample
image_name

the image name of the Visium assay, Default: main
channel_name

the channel name of the image of the Visium assay, Default: H&E
...

additional parameters passed to formVoltRon

importVisium

Description

Importing Visium data

Usage

importVisium(
  dir.path,
  selected_assay = "Gene Expression",
  assay_name = "Visium",
  sample_name = NULL,
  image_name = "main",
  channel_name = "H&E",
  inTissue = TRUE,
  resolution_level = "lowres",
  ...
)

Arguments

dir.path

path to Visium output folder
selected_assay

selected assay from Visium
assay_name

the assay name
sample_name

the name of the sample
image_name

the image name of the Visium assay, Default: main
channel_name

the channel name of the image of the Visium assay, Default: H&E
inTissue

if TRUE, only barcodes that are in the tissue will be kept (default: TRUE)
resolution_level

the level of resolution of Visium image: "lowres" (default) or "hires"
...

additional parameters passed to formVoltRon

importVisiumHD

Description

Importing VisiumHD data

Usage

importVisiumHD(
  dir.path,
  bin.size = "8",
  selected_assay = "Gene Expression",
  assay_name = "VisiumHD",
  sample_name = NULL,
  image_name = "main",
  channel_name = "H&E",
  inTissue = TRUE,
  resolution_level = "lowres",
  ...
)

Arguments

dir.path

path to Visium output folder
bin.size

bin size of the VisiumHD output (Exp: "2", "8" and "16")
selected_assay

selected assay from Visium
assay_name

the assay name
sample_name

the name of the sample
image_name

the image name of the Visium assay, Default: main
channel_name

the channel name of the image of the Visium assay, Default: H&E
inTissue

if TRUE, only barcodes that are in the tissue will be kept (default: TRUE)
resolution_level

the level of resolution of Visium image: "lowres" (default) or "hires"
...

additional parameters passed to formVoltRon

importXenium

Description

Importing Xenium data

Usage

importXenium(
  dir.path,
  selected_assay = "Gene Expression",
  assay_name = "Xenium",
  sample_name = NULL,
  use_image = TRUE,
  morphology_image = "morphology_lowres.tif",
  resolution_level = 7,
  overwrite_resolution = TRUE,
  image_name = "main",
  channel_name = "DAPI",
  import_molecules = FALSE,
  verbose = TRUE,
  ...
)

Arguments

dir.path

path to Xenium output folder
selected_assay

selected assay from Xenium
assay_name

the assay name of the SR object
sample_name

the name of the sample
use_image

if TRUE, the DAPI image will be used.
morphology_image

the name of the lowred morphology image. Default: morphology_lowres.tif
resolution_level

the level of resolution within Xenium OME-TIFF image, see generateXeniumImage. Default: 7 (553x402)
overwrite_resolution

if TRUE, the image "file.name" will be generated again although it exists at "dir.path"
image_name

the image name of the Xenium assay, Default: main
channel_name

the channel name of the image of the Xenium assay, Default: DAPI
import_molecules

if TRUE, molecule assay will be created along with cell assay.
verbose

verbose
...

additional parameters passed to formVoltRon

knn_annoy

Description

knn engine employed by RcppAnnoy package, adapted from BPCells package.

Usage

knn_annoy(data, query = data, k = 10, n_trees = 50, search_k = -1)

Arguments

data

data
query

query data (Default: data)
k

number of neighbors for kNN
n_trees

Number of trees during index build time. More trees gives higher accuracy
search_k

Number of nodes to inspect during the query, or -1 for default value. Higher number gives higher accuracy

Details

**knn_annoy**: Use RcppAnnoy as knn engine

loadVoltRon

Description

load VoltRon object from memory or disk

Usage

loadVoltRon(dir = "my_se")

Arguments

dir

the directory that VoltRon object is found.

Example MELC Data

Description

This VoltRon object is used for testing and as an example

Usage

melc_data

Format

An object of class VoltRon of length 1.

Source

Created to serve as an example.

Examples

data(melc_data)

Merging VoltRon objects

Description

Given a VoltRon object, and a list of VoltRon objects, merge all.

Usage

## S4 method for signature 'VoltRon,ANY'
merge(x, y, samples = NULL, main.assay = NULL, verbose = TRUE)

Arguments

x

a VoltRon Object
y

a single or a list of VoltRon objects
samples

a single sample name or multiple sample names of the same size as the given VoltRon objects
main.assay

the name of the main assay
verbose

verbose

Merging vrBlock objects

Description

Given a vrBlock object, and a list of vrSample objects, merge all.

Usage

## S4 method for signature 'vrBlock,ANY'
merge(x, y, samples = NULL)

Arguments

x

a vrSample object
y

a list of vrSample objects
samples

the sample names

Merging vrMetadata objects

Description

Given a vrMetadata object, and a list of vrMetadata objects, merge all.

Usage

## S4 method for signature 'vrMetadata,ANY'
merge(x, y)

Arguments

x

a vrMetadata object
y

a single or a list of vrMetadata objects

Merging vrSample objects

Description

Given a vrSample object, and a list of vrSample objects, merge all.

Usage

## S4 method for signature 'vrSample,ANY'
merge(x, y, samples = NULL)

Arguments

x

a vrSample object
y

a list of vrSample objects
samples

the sample names

Example Transfer Data

Description

This VoltRon object is used for testing and as an example for transfering information between layers and multilayer plotting.

Usage

merged_object

Format

An object of class VoltRon of length 1.

Source

Created to serve as an example.

Examples

data(merged_object)

Metadata

Description

Get the metadata of a VoltRon object.

Usage

Metadata(object, ...)

Metadata(object, ...) <- value

## S4 method for signature 'VoltRon'
Metadata(object, assay = NULL, type = NULL)

## S4 replacement method for signature 'VoltRon'
Metadata(object, assay = NULL, type = NULL) <- value

Arguments

object

a VoltRon object.
...

arguments passed to other methods.
value

new metadata
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
type

the assay type: ROI, spot or cell, or all for the entire metadata object

modulateImage

Description

Modulating Magick images

Usage

modulateImage(object, ...)

## S4 method for signature 'VoltRon'
modulateImage(
  object,
  assay = NULL,
  name = NULL,
  reg = FALSE,
  channel = NULL,
  brightness = 100,
  saturation = 100,
  hue = 100,
  force = FALSE
)

## S4 method for signature 'vrAssay'
modulateImage(
  object,
  name = NULL,
  reg = FALSE,
  channel = NULL,
  brightness = 100,
  saturation = 100,
  hue = 100,
  force = FALSE
)

## S4 method for signature 'vrAssayV2'
modulateImage(
  object,
  name = NULL,
  reg = FALSE,
  channel = NULL,
  brightness = 100,
  saturation = 100,
  hue = 100,
  force = FALSE
)

## S4 method for signature 'vrImage'
modulateImage(
  object,
  channel = NULL,
  brightness = 100,
  saturation = 100,
  hue = 100,
  force = FALSE
)

## S4 method for signature 'vrSpatial'
modulateImage(
  object,
  channel = NULL,
  brightness = 100,
  saturation = 100,
  hue = 100,
  force = FALSE
)

Arguments

object

a VoltRon, vrAssay or vrSpatial object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
name

the name of the image
reg

TRUE if registered coordinates of the main image (vrMainSpatial) is requested
channel

the name of the channel associated with the image
brightness

modulation of brightness as percentage of the current value (100 for no change)
saturation

modulation of saturation as percentage of the current value (100 for no change)
hue

modulation of hue is an absolute rotation of -180 degrees to +180 degrees from the current position corresponding to an argument range of 0 to 200 (100 for no change)
force

if TRUE, all channels will be modulated given no specific channel name

Normalize Data

Description

Given a VoltRon or vrAssay object, normalize the raw count data.

Usage

normalizeData(object, ...)

## S4 method for signature 'VoltRon'
normalizeData(
  object,
  assay = NULL,
  method = "LogNorm",
  desiredQuantile = 0.9,
  scale = 0.2,
  sizefactor = 10000,
  feat_type = NULL
)

## S4 method for signature 'vrAssay'
normalizeData(
  object,
  method = "LogNorm",
  desiredQuantile = 0.9,
  scale = 0.2,
  sizefactor = 10000,
  feat_type = NULL
)

## S4 method for signature 'vrAssayV2'
normalizeData(
  object,
  method = "LogNorm",
  desiredQuantile = 0.9,
  scale = 0.2,
  sizefactor = 10000,
  feat_type = NULL
)

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class if NULL, the default assay will be used, see vrMainAssay.
method

the normalization method: "LogNorm", "Q3Norm", "LogQ3Norm", "CLR" or "hyper.arcsine".
desiredQuantile

the quantile of the data if "QuanNorm" or "LogQuanNorm" is selected as method.
scale

the scale parameter for the hyperbolic arcsine transformation
sizefactor

size factor if method is selected as LogNorm
feat_type

the feature set type

open_zarr

Description

open zarr store

Usage

open_zarr(dir, name)

Arguments

dir

the location of zarr store
name

name of the zarr store

registerSpatialData

Description

A mini shiny app for registering images and spatial coordinates of multiple consecutive VoltRon objects.

Usage

registerSpatialData(
  object_list = NULL,
  reference_spatdata = NULL,
  query_spatdata = NULL,
  keypoints = NULL,
  mapping_parameters = list(),
  interactive = TRUE,
  shiny.options = list(launch.browser = getOption("shiny.launch.browser", interactive()))
)

Arguments

object_list

a list of VoltRon (or Seurat) objects
reference_spatdata

a reference spatial data set, used only if object_list is NULL
query_spatdata

a query spatial data set, used only if object_list is NULL
keypoints

(DEPRECATED) a list of tables, each points to matching keypoints from registered images.
mapping_parameters

for manual image registration, a list of tables, each points to matching keypoints from registered images, and for automated image registration, a set of mapping parameters
interactive

if TRUE, the shiny application for image registration will be triggered, otherwise 'mapping_parameters' or 'keypoints' should be defined.
shiny.options

a list of shiny options (launch.browser, host, port etc.) passed options arguement of shinyApp. For more information, see runApp

resizeImage

Description

Resizing Magick images

Usage

resizeImage(object, ...)

## S4 method for signature 'VoltRon'
resizeImage(object, assay = NULL, name = NULL, reg = FALSE, size = NULL)

## S4 method for signature 'vrAssay'
resizeImage(object, name = NULL, reg = FALSE, size = NULL)

## S4 method for signature 'vrAssayV2'
resizeImage(object, name = NULL, reg = FALSE, size = NULL)

## S4 method for signature 'vrImage'
resizeImage(object, size = NULL)

## S4 method for signature 'vrSpatial'
resizeImage(object, size = NULL)

Arguments

object

a VoltRon, vrAssay or vrSpatial object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
name

the name of the image
reg

TRUE if registered coordinates of the main image (vrMainSpatial) is requested
size

the width of the resized image

SampleMetadata

Description

Get the sample metadata of a VoltRon object

Usage

SampleMetadata(object)

Arguments

object

a VoltRon object

saveVoltRon

Description

save VoltRon object in memory or on disk

Usage

saveVoltRon(
  object,
  assay = NULL,
  format = c("InMemoryVoltRon", "HDF5VoltRon", "ZarrVoltRon"),
  output = NULL,
  replace = FALSE,
  chunkdim = NULL,
  level = NULL,
  as.sparse = FALSE,
  verbose = TRUE,
  feature.vs.obs.engine = "BPCells"
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata.
format

the format the object should be written: InMemoryVoltRon (rds only), HDF5VoltRon (h5), or ZarrVoltRon (zarr).
output

When saving, the directory will be created if it doesn't already exist. If the directory already exists and no prefix is specified and replace is set to TRUE, then it's replaced with an empty directory.
replace

When no prefix is specified, should a pre-existing directory be replaced with a new empty one? The content of the pre-existing directory will be lost!
chunkdim

The dimensions of the chunks to use for writing the assay data to disk.
level

The compression level to use for writing the assay data to disk.
as.sparse

Whether the dataset (for HDF5 DelayedArray) should be flagged as sparse or not.
verbose

verbose
feature.vs.obs.engine

The on-disk method for the manipulating feature x obs matrices: BPCells or DelayedArray

slotApply

Description

apply to slots

Usage

slotApply(x, FUN, ...)

Arguments

x

object
FUN

function
...

arguments passed to FUN

slotToList

Description

slot to list

Usage

slotToList(x)

Arguments

x

object

Subsetting VoltRon objects

Description

Given a VoltRon object, subset the object given one of the attributes

Usage

## S4 method for signature 'VoltRon'
subset(
  x,
  subset,
  samples = NULL,
  assays = NULL,
  spatialpoints = NULL,
  features = NULL,
  image = NULL,
  interactive = FALSE,
  use.points.only = FALSE,
  shiny.options = list(launch.browser = getOption("shiny.launch.browser", interactive()))
)

Arguments

x

a VoltRon object
subset

Logical statement for subsetting
samples

the set of samples to subset the object
assays

the set of assays to subset the object
spatialpoints

the set of spatial points to subset the object
features

the set of features to subset the object
image

the subseting string passed to image_crop
interactive

TRUE if interactive subsetting on the image is demanded
use.points.only

if interactive is TRUE, use spatial points instead of the reference image
shiny.options

a list of shiny options (launch.browser, host, port etc.) passed options arguement of shinyApp. For more information, see runApp

Examples

# example data
data("visium_data")

# subset based on assay
subset(visium_data, assays = "Assay1")
subset(visium_data, assays = "Visium")

# subset based on samples
subset(visium_data, samples = "Anterior1")

# subset based on assay
subset(visium_data, spatialpoints = c("GTTATATTATCTCCCT-1_Assay1", "GTTTGGGTTTCGCCCG-1_Assay1"))

# subset based on features
subset(visium_data, features = c("Map3k19", "Rab3gap1"))

# interactive subsetting
## Not run: 
visium_subset_data <- subset(visium_data, interactive = TRUE)
visium_subset <- visium_subset_data$subsets[[1]]

## End(Not run)

Subsetting vrAssay objects

Description

Given a vrAssay object, subset the object given one of the attributes

Usage

## S4 method for signature 'vrAssay'
subset(x, subset, spatialpoints = NULL, features = NULL, image = NULL)

Arguments

x

a vrAssay object
subset

Logical statement for subsetting
spatialpoints

the set of spatial points to subset the object
features

the set of features to subset the object
image

the subseting string passed to image_crop

Subsetting vrAssayV2 objects

Description

Given a vrAssayV2 object, subset the object given one of the attributes

Usage

## S4 method for signature 'vrAssayV2'
subset(x, subset, spatialpoints = NULL, features = NULL, image = NULL)

Arguments

x

a vrAssayV2 object
subset

Logical statement for subsetting
spatialpoints

the set of spatial points to subset the object
features

the set of features to subset the object
image

the subseting string passed to image_crop

Subsetting vrBlock objects

Description

Given a vrBlock object, subset the object given one of the attributes

Usage

## S4 method for signature 'vrBlock'
subset(x, subset, assays = NULL, spatialpoints = NULL, image = NULL)

Arguments

x

a vrSample object
subset

the subset statement
assays

the set of assays to subset the object
spatialpoints

the set of spatial points to subset the object
image

the subseting string passed to image_crop

Subsetting vrImage objects

Description

Given a vrImage object, subset the object given one of the attributes.

Usage

## S4 method for signature 'vrImage'
subset(x, subset, spatialpoints = NULL, image = NULL)

Arguments

x

A vrImage object
subset

Logical statement for subsetting
spatialpoints

the set of spatial points to subset the object
image

the subseting string passed to image_crop

Subsetting vrLayer objects

Description

Given a vrLayer object, subset the object given one of the attributes

Usage

## S4 method for signature 'vrLayer'
subset(x, subset, assays = NULL, spatialpoints = NULL, image = NULL)

Arguments

x

a vrLayer object
subset

the subset statement
assays

the set of assays to subset the object
spatialpoints

the set of spatial points to subset the object
image

the subseting string passed to image_crop

Subsetting vrMetadata objects

Description

Given a vrMetadata object, subset the object given one of the attributes

Usage

## S4 method for signature 'vrMetadata'
subset(x, subset, samples = NULL, assays = NULL, spatialpoints = NULL)

Arguments

x

a vrMetadata object
subset

the subset statement
samples

the set of samples to subset the object
assays

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata(object)
spatialpoints

the set of spatial points to subset the object

Subsetting vrSample objects

Description

Given a vrSample object, subset the object given one of the attributes

Usage

## S4 method for signature 'vrSample'
subset(x, subset, assays = NULL, spatialpoints = NULL, image = NULL)

Arguments

x

a vrSample object
subset

the subset statement
assays

the set of assays to subset the object
spatialpoints

the set of spatial points to subset the object
image

the subseting string passed to image_crop

Subsetting vrSpatial objects

Description

Given a vrSpatial object, subset the object given one of the attributes.

Usage

## S4 method for signature 'vrSpatial'
subset(x, subset, spatialpoints = NULL, image = NULL)

Arguments

x

A vrSpatial object
subset

Logical statement for subsetting
spatialpoints

the set of spatial points to subset the object
image

the subseting string passed to image_crop

subsetCoordinates

Description

subsetting coordinates given cropping parameters of a magick image objects

Usage

subsetCoordinates(coords, imageinfo, crop_info)

Arguments

coords

the coordinates of the spatial points
imageinfo

the magick image info associated with the image
crop_info

the subseting string passed to image_crop

subsetSegments

Description

subsetting segments given cropping parameters of a magick image objects

Usage

subsetSegments(segments, imageinfo, crop_info)

Arguments

segments

the list of segments each associated with a spatial point
imageinfo

the magick image info associated with the image
crop_info

the subseting string passed to image_crop

transferData

Description

transfer data across assays

Usage

transferData(
  object,
  from = NULL,
  to = NULL,
  features = NULL,
  expand = NULL,
  new_feature_name = NULL
)

Arguments

object

a VoltRon object
from

the name or class of assay whose data transfered to the second assay
to

the name or class of target assay where data is transfered to
features

the set of features from vrFeatures or metadata columns from Metadata that are transferred. Only one metadata feature can be transfered at a time.
expand

if TRUE, metadata features will be transformed into dummy features where each category in the feature will be a new feature. If FALSE, metadata features will not be transformed and transfered as metadata columns, else the decision will be made automatically.
new_feature_name

the name of the new feature set created from the source assay defined in from argument. Only used when a new assay in created.

Update Assay

Description

update assays from vrAssay to vrAssayV2

Usage

updateAssay(object, ...)

## S4 method for signature 'vrAssay'
updateAssay(object)

## S4 method for signature 'vrAssayV2'
updateAssay(object)

## S4 method for signature 'VoltRon'
updateAssay(object, assay = NULL)

Arguments

object

a vrAssayV2 object to be converted to vrAssayV2
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.

Example Visium Data

Description

This VoltRon object is used for testing and as an example

Usage

visium_data

Format

An object of class VoltRon of length 1.

Source

Created to serve as an example.

Examples

data(visium_data)

The VoltRon Class

Description

The VoltRon Class

Slots

samples

A list of samples (vrSample)

metadata

A vrMetadata object that includes metadata of ROIs, spots, and cells

sample.metadata

Contains meta-information about each sample, layer and assay

graph

A igraph object

main.assay

The type of the main assay (i.e. Visium, Xenium, GeoMx etc.)

project

Name of the project

Methods for VoltRon

Description

Methods for VoltRon objects for generics defined in other packages

Usage

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

## S3 replacement method for class 'VoltRon'
x$i <- value

## S3 method for class 'VoltRon'
.DollarNames(x, pattern = "")

## S4 method for signature 'VoltRon,character,missing'
x[[i, j, ...]]

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

## S4 method for signature 'VoltRon,character,character'
x[[i, j, ...]]

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

Arguments

x

A VoltRon object
i, value

Depends on the usage

$, $<-

Name (i) of a single metadata column from the main assay, see vrMainAssay

[[, [[<-

If only i is given, either a vrSample object or a vrAssay for i (and value) being name of the sample or assay. If both i and j are given, vrLayer with layer name j (and value) of vrSample with same name i.

...

Arguments passed to other methods
pattern

A regular expression. Only matching names are returned.

j

Depends on the usage, see i.

Value

[[<-: x with the metadata or associated objects added as i; if value is NULL, removes metadata or associated object i from object x

[[<-: x with the metadata or associated objects added as i; if value is NULL, removes metadata or associated object i from object x

Functions

  • $: Metadata access for VoltRon objects

  • `$`(VoltRon) <- value: Metadata overwrite for VoltRon objects

  • .DollarNames(VoltRon): Autocompletion for $ access for VoltRon objects

  • x[[i: Accessing vrAssay or vrSample objects from VoltRon objects

  • `[[`(x = VoltRon, i = character, j = missing) <- value: Overwriting vrAssay or vrSample objects from VoltRon objects

  • x[[i: Accessing vrLayer objects from VoltRon objects

  • `[[`(x = VoltRon, i = character, j = character) <- value: Overwriting vrLayer objects from VoltRon objects

The vrAssay (VoltRon Assay) Class

Description

The vrAssay (VoltRon Assay) Class

Slots

rawdata

raw data

normdata

normalized data

featuredata

feature metadata

embeddings

list of embeddings

image

a list of vrImage objects

params

additional parameters used by different assay types

type

the type of the assay (tile, molecule, cell, spot, ROI)

name

the assay name

main_image

the key of the main image

Get Assay names

Description

Given a VoltRon, vrMetadata or vrAssay object, get/set names of assays.

Usage

vrAssayNames(object, ...)

## S4 method for signature 'VoltRon'
vrAssayNames(object, assay = NULL)

## S4 method for signature 'vrMetadata'
vrAssayNames(object)

## S4 method for signature 'vrAssay'
vrAssayNames(object)

## S4 method for signature 'vrAssayV2'
vrAssayNames(object)

## S4 replacement method for signature 'vrAssay'
vrAssayNames(object) <- value

## S4 replacement method for signature 'vrAssayV2'
vrAssayNames(object) <- value

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
value

assay name

Get assay parameters

Description

Given a vrAssay object, if there are any, get a list of parameters of the assay(s)

Usage

vrAssayParams(object, param = NULL)

Arguments

object

a vrAssay object
param

the parameter value to return

Get assay types

Description

Given a VoltRon or vrAssay object, get types of assays. Here, an assay type is of either tile, molecule, cell, spot or ROI.

Usage

vrAssayTypes(object, ...)

## S4 method for signature 'VoltRon'
vrAssayTypes(object, assay = NULL)

## S4 method for signature 'vrAssay'
vrAssayTypes(object)

## S4 method for signature 'vrAssayV2'
vrAssayTypes(object)

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.

The vrAssayV2 (VoltRon Assay) Class

Description

The vrAssayV2 (VoltRon Assay) Class

Slots

data

list of count/normalized datasets

featuredata

list of feature metadata

embeddings

list of embeddings

image

a list of vrImage objects

params

additional parameters used by different assay types

type

the type of the assay (tile, molecule, cell, spot, ROI)

name

the assay name

main_image

the key of the main image

main_featureset

the key of the main feature set

vrBarPlot

Description

vrBarPlot

Usage

vrBarPlot(
  object,
  features = NULL,
  assay = NULL,
  x.label = NULL,
  group.by = "Sample",
  split.by = NULL,
  norm = TRUE,
  log = FALSE,
  ncol = 2,
  nrow = NULL
)

Arguments

object

a VoltRon object
features

a set of features to be visualized, either from vrFeatures of raw or normalized data or columns of the Metadata.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
x.label

labels of the x axis
group.by

a column of metadata from Metadata used as grouping label for the spatial entities
split.by

the column to split the barplots by
norm

if TRUE, the normalized data is used
log

if TRUE, data features (excluding metadata features) will be log transformed
ncol

column wise number of plots, for ggarrange
nrow

row wise number of plots, for ggarrange

The vrBlock (VoltRon Block) Class

Description

The vrBlock (VoltRon Block) Class

Slots

layer

A list of layers (vrLayer)

zlocation

a vector of z coordinates of layers

adjacency

an adjacency matrix of connected layers within a block

vrCoordinates

Description

Given a VoltRon, vrAssay or vrSpatial object, get and set the coordinates of assays and coordinate systems

Usage

vrCoordinates(object, ...)

## S4 method for signature 'VoltRon'
vrCoordinates(
  object,
  assay = NULL,
  image_name = NULL,
  spatial_name = NULL,
  reg = FALSE
)

## S4 method for signature 'vrAssay'
vrCoordinates(object, image_name = NULL, spatial_name = NULL, reg = FALSE)

## S4 method for signature 'vrAssayV2'
vrCoordinates(object, image_name = NULL, spatial_name = NULL, reg = FALSE)

## S4 method for signature 'vrImage'
vrCoordinates(object)

## S4 method for signature 'vrSpatial'
vrCoordinates(object)

## S4 replacement method for signature 'VoltRon'
vrCoordinates(object, image_name = NULL, spatial_name = NULL, reg = FALSE) <- value

## S4 replacement method for signature 'vrAssay'
vrCoordinates(object, image_name = NULL, spatial_name = NULL, reg = FALSE) <- value

## S4 replacement method for signature 'vrAssayV2'
vrCoordinates(object, image_name = NULL, spatial_name = NULL, reg = FALSE) <- value

## S4 replacement method for signature 'vrImage'
vrCoordinates(object) <- value

## S4 replacement method for signature 'vrSpatial'
vrCoordinates(object) <- value

vrCoordinates(object, ...) <- value

Arguments

object

a VoltRon, vrAssay or vrSpatial object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
image_name

(deprecated, use spatial_name) the name/key of the image associated with the coordinates
spatial_name

the name/key of the spatial system associated with the coordinates
reg

TRUE if registered coordinates of the main image (vrMainImage) is requested
value

coordinates

vrData

Description

Get data of assays

Usage

vrData(object, ...)

## S4 method for signature 'VoltRon'
vrData(
  object,
  assay = NULL,
  features = NULL,
  feat_type = NULL,
  norm = FALSE,
  ...
)

## S4 method for signature 'vrAssay'
vrData(object, features = NULL, feat_type = NULL, norm = FALSE, ...)

## S4 method for signature 'vrAssayV2'
vrData(object, features = NULL, feat_type = NULL, norm = FALSE, ...)

Arguments

object

a VoltRon or vrAssay object.
...

additional parameters passed to other methods and vrImages
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
features

the set of features
feat_type

the feature set type
norm

TRUE if normalized data should be returned

vrEmbeddingFeaturePlot

Description

Plotting features of spatially resolved cells and spots on embeddings from multiple assays in a VoltRon object.

Usage

vrEmbeddingFeaturePlot(
  object,
  embedding = "pca",
  features = NULL,
  combine.features = FALSE,
  n.tile = NULL,
  norm = TRUE,
  log = FALSE,
  assay = NULL,
  ncol = 2,
  nrow = NULL,
  font.size = 2,
  pt.size = 1,
  shape = 16,
  keep.scale = "feature",
  common.legend = TRUE,
  collapse.plots = TRUE
)

Arguments

object

a VoltRon object
embedding

the embedding type, i.e. pca, umap etc.
features

a set of features to be visualized, either from vrFeatures of raw or normalized data or columns of the Metadata.
combine.features

whether to combine all features in one plot
n.tile

The number of tiles on x-and y-axis for rasterizing points (see geom_tile). The rasterization is performed automatically for large number of points Only applicable to spots, cells and molecules. If n.tile = 0 will turn of automated rasterization.
norm

if TRUE, the normalized data is used
log

if TRUE, data features (excluding metadata features) will be log transformed
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
ncol

column wise number of plots, for ggarrange
nrow

row wise number of plots, for ggarrange
font.size

font size
pt.size

point size
shape

shape
keep.scale

whether unify all scales for all features or not
common.legend

whether to use a common legend for all plots, see ggarrange
collapse.plots

whether to combine all ggplots

Get Embedding names

Description

Given a VoltRon or vrAssay object, give names of embeddings

Usage

vrEmbeddingNames(object, ...)

## S4 method for signature 'VoltRon'
vrEmbeddingNames(object, assay = NULL)

## S4 method for signature 'vrAssay'
vrEmbeddingNames(object)

## S4 method for signature 'vrAssayV2'
vrEmbeddingNames(object)

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.

vrEmbeddingPlot

Description

Plotting embeddings of cells and spots on associated images from multiple assays in a VoltRon object.

Usage

vrEmbeddingPlot(
  object,
  embedding = "pca",
  group.by = "Sample",
  group.ids = NULL,
  split.by = NULL,
  colors = NULL,
  n.tile = NULL,
  assay = NULL,
  ncol = 2,
  nrow = NULL,
  font.size = 5,
  pt.size = 1,
  shape = 16,
  label = FALSE,
  common.legend = TRUE,
  collapse.plots = TRUE
)

Arguments

object

a VoltRon object
embedding

the embedding type, i.e. pca, umap etc.
group.by

a column of metadata from Metadata used as grouping label for the spatial entities
group.ids

a subset of categories defined in metadata column from group.by
split.by

a column of metadata from Metadata used as splitting spatial entities into ggplot panels, see facet_wrap
colors

the color set for group.by. Should be of the same size of group.id (if specified) or unique elements in group.by
n.tile

The number of tiles on x-and y-axis for rasterizing points (see geom_tile). The rasterization is performed automatically for large number of points Only applicable to spots, cells and molecules. If n.tile = 0 will turn of automated rasterization.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
ncol

column wise number of plots, for facet_wrap
nrow

row wise number of plots, for facet_wrap
font.size

font size of labels, if label is TRUE
pt.size

point size
shape

shape
label

if TRUE, the labels of the ROI assays will be visualized
common.legend

whether to use a common legend for all plots, see ggarrange
collapse.plots

whether to combine all ggplots

vrEmbeddings

Description

Given a VoltRon or vrAssay object, get embeddings of spatial points

Usage

vrEmbeddings(object, ...)

## S4 method for signature 'VoltRon'
vrEmbeddings(object, assay = NULL, type = "pca", dims = seq_len(30))

## S4 method for signature 'vrAssay'
vrEmbeddings(object, type = "pca", dims = seq_len(30))

## S4 method for signature 'vrAssayV2'
vrEmbeddings(object, type = "pca", dims = seq_len(30))

## S4 replacement method for signature 'vrAssay'
vrEmbeddings(object, type = "pca") <- value

## S4 replacement method for signature 'vrAssayV2'
vrEmbeddings(object, type = "pca") <- value

## S4 replacement method for signature 'VoltRon'
vrEmbeddings(object, assay = NULL, type = "pca", overwrite = FALSE) <- value

vrEmbeddings(object, ...) <- value

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
type

the key name for the embedding
dims

the set of dimensions of the embedding data
value

new embedding data
overwrite

Whether the existing embedding with name 'type' should be overwritten

Feature Data

Description

Get and set feature data from the main.assay

Usage

vrFeatureData(object, ...)

## S4 method for signature 'VoltRon'
vrFeatureData(object, assay = NULL, feat_type = NULL)

## S4 method for signature 'vrAssay'
vrFeatureData(object)

## S4 method for signature 'vrAssayV2'
vrFeatureData(object, feat_type = NULL)

## S4 replacement method for signature 'VoltRon'
vrFeatureData(object, assay = NULL) <- value

## S4 replacement method for signature 'vrAssay'
vrFeatureData(object) <- value

## S4 replacement method for signature 'vrAssayV2'
vrFeatureData(object, feat_type = NULL) <- value

vrFeatureData(object, ...) <- value

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
feat_type

the feature set type
value

new feature metadata

vrFeatures

Description

Get names of the features.

Usage

vrFeatures(object, ...)

## S4 method for signature 'VoltRon'
vrFeatures(object, assay = NULL)

## S4 method for signature 'vrAssay'
vrFeatures(object)

## S4 method for signature 'vrAssayV2'
vrFeatures(object)

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.

vrFeatureTypeNames

Description

Get the names of the feature types

Usage

vrFeatureTypeNames(object, ...)

## S4 method for signature 'vrAssayV2'
vrFeatureTypeNames(object)

## S4 method for signature 'vrAssay'
vrFeatureTypeNames(object)

## S4 method for signature 'VoltRon'
vrFeatureTypeNames(object, assay = NULL)

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. If NULL, the default assay will be used, see vrMainAssay. If given as "all", then provides a summary of spatial systems across all assays

vrGraph

Description

Get graph of a VoltRon object

Usage

vrGraph(object, assay = NULL, graph.type = NULL)

vrGraph(object, assay = NULL, graph.type = "kNN") <- value

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
graph.type

the type of the graph, either custom or given by getProfileNeighbors or getSpatialNeighbors functions
value

new graph

vrGraphNames

Description

Get names of all graphs

Usage

vrGraphNames(object, assay = NULL)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.

HeatmapPlot

Description

HeatmapPlot

Usage

vrHeatmapPlot(
  object,
  assay = NULL,
  features = NULL,
  group.by = "clusters",
  norm = TRUE,
  scaled = TRUE,
  show_row_names = NULL,
  cluster_rows = TRUE,
  show_heatmap_legend = FALSE,
  outlier.quantile = 0.99,
  highlight.some = FALSE,
  n_highlight = 30,
  font.size = 13.2,
  ...
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
features

a set of features to be visualized from vrFeatures of raw or normalized data.
group.by

a column of metadata from Metadata used as grouping label for the spatial entities
norm

if TRUE, the normalized data is used
scaled

if TRUE, the data will be scaled before visualization
show_row_names

if TRUE, row names of the heatmap will be shown
cluster_rows

if TRUE, the rows of the heatmap will be clustered
show_heatmap_legend

if TRUE, the heatmap legend is shown
outlier.quantile

quantile for detecting outliers whose values are set to the quantile, change to lower values to adjust large number of outliers, default: 0.99
highlight.some

if TRUE, some rows will be showed at random, reproducible by seed argument
n_highlight

the number of row labels shown, if show_row_names is TRUE
font.size

font size
...

additional parameters passed to getVariableFeatures

The vrImage (VoltRon Image) Class

Description

The vrImage (VoltRon Image) Class

Slots

coords

spatial coordinates of the assay

segments

spatial coordinates of the segments, if available

image

image of the spatial assay, bitmap class

main_channel

the key of the main channel of vrImage object

vrImageChannelNames

Description

Get names of all image channels

Usage

vrImageChannelNames(object, ...)

## S4 method for signature 'VoltRon'
vrImageChannelNames(object, assay = NULL)

## S4 method for signature 'vrAssay'
vrImageChannelNames(object, name = NULL)

## S4 method for signature 'vrAssayV2'
vrImageChannelNames(object, name = NULL)

## S4 method for signature 'vrImage'
vrImageChannelNames(object, return.report = TRUE)

## S4 method for signature 'vrSpatial'
vrImageChannelNames(object, return.report = TRUE)

Arguments

object

a VoltRon, vrAssay or vrSpatial object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
name

the key of the image
return.report

if TRUE and no image is present, return a character stating that there is no image

vrImageNames

Description

Get names of all images

Usage

vrImageNames(object, ...)

## S4 method for signature 'VoltRon'
vrImageNames(object, assay = NULL)

## S4 method for signature 'vrAssay'
vrImageNames(object)

## S4 method for signature 'vrAssayV2'
vrImageNames(object)

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. If NULL, the default assay will be used, see vrMainAssay. If equals to "all", then provides a summary of spatial systems across all assays

vrImages

Description

Get images of VoltRon objects

Usage

vrImages(object, ...)

## S4 method for signature 'VoltRon'
vrImages(
  object,
  assay = NULL,
  name = NULL,
  reg = FALSE,
  channel = NULL,
  as.raster = FALSE,
  scale.perc = 100
)

## S4 method for signature 'vrAssay'
vrImages(
  object,
  name = NULL,
  reg = FALSE,
  channel = NULL,
  as.raster = FALSE,
  scale.perc = 100
)

## S4 method for signature 'vrAssayV2'
vrImages(
  object,
  name = NULL,
  reg = FALSE,
  channel = NULL,
  as.raster = FALSE,
  scale.perc = 100
)

## S4 method for signature 'vrImage'
vrImages(object, channel = NULL, as.raster = FALSE, scale.perc = 100)

## S4 method for signature 'vrSpatial'
vrImages(object, channel = NULL, as.raster = FALSE, scale.perc = 100)

## S4 replacement method for signature 'vrAssay'
vrImages(object, name = NULL, channel = NULL, reg = FALSE) <- value

## S4 replacement method for signature 'vrAssayV2'
vrImages(object, name = NULL, channel = NULL, reg = FALSE) <- value

## S4 replacement method for signature 'vrImage'
vrImages(object, channel = NULL) <- value

## S4 replacement method for signature 'vrSpatial'
vrImages(object, channel = NULL) <- value

vrImages(object, ...) <- value

Arguments

object

a VoltRon, vrAssay or vrSpatial object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
name

the name of the main spatial system
reg

TRUE if registered coordinates of the main image (vrMainSpatial) is requested
channel

the name of the channel associated with the image
as.raster

return as raster
scale.perc

scale percentage if lower resolution image needed
value

a raster image or an image of magick-image object

The vrLayer (VoltRon Layer) Class

Description

The vrLayer (VoltRon Layer) Class

Slots

assay

A list of assays (vrAssay)

connectivity

the connectivity graph

Methods for vrLayer objects

Description

Methods for vrLayer objects for generics defined in other packages

Usage

## S4 method for signature 'vrLayer,character,ANY'
x[[i]]

## S4 replacement method for signature 'vrLayer,character,ANY'
x[[i]] <- value

Arguments

x

A vrLayer object
i

the name of assay associated with the layer, see SampleMetadata
value

a vrAssayV2 object, see vrAssayV2

Functions

  • x[[i: Accessing vrAssay objects from vrLayer objects

  • `[[`(x = vrLayer, i = character, j = ANY) <- value: Overwriting vrAssay objects from vrLayer objects

Main Assay

Description

Get and set the main assay of a VoltRon object

Get and set the main assay of a VoltRon object

Usage

vrMainAssay(object, ...)

vrMainAssay(object, ...) <- value

## S4 method for signature 'VoltRon'
vrMainAssay(object)

## S4 replacement method for signature 'VoltRon'
vrMainAssay(object) <- value

Arguments

object

a VoltRon object
...

arguments passed to other methods.
value

new assay name

vrMainChannel

Description

Get and set the main channel name of the spatial system.

Usage

vrMainChannel(object, ...)

## S4 method for signature 'vrAssay'
vrMainChannel(object, name = NULL)

## S4 method for signature 'vrAssayV2'
vrMainChannel(object, name = NULL)

## S4 method for signature 'vrImage'
vrMainChannel(object)

## S4 method for signature 'vrSpatial'
vrMainChannel(object)

## S4 replacement method for signature 'vrAssay'
vrMainChannel(object, name = NULL) <- value

## S4 replacement method for signature 'vrAssayV2'
vrMainChannel(object, name = NULL) <- value

## S4 replacement method for signature 'vrImage'
vrMainChannel(object) <- value

## S4 replacement method for signature 'vrSpatial'
vrMainChannel(object) <- value

vrMainChannel(object, ...) <- value

Arguments

object

a vrAssay or vrSpatial object
...

arguments passed to other methods.
name

the name of the image
value

the name of main channel of the spatial system

vrMainFeatureType

Description

Get the main feature type

Set the main image

Usage

vrMainFeatureType(object, ...)

## S4 method for signature 'VoltRon'
vrMainFeatureType(object, assay = NULL)

## S4 method for signature 'vrAssayV2'
vrMainFeatureType(object)

## S4 method for signature 'vrAssay'
vrMainFeatureType(object)

## S4 replacement method for signature 'VoltRon'
vrMainFeatureType(object, assay = NULL) <- value

## S4 replacement method for signature 'vrAssayV2'
vrMainFeatureType(object, ignore = FALSE) <- value

## S4 replacement method for signature 'vrAssay'
vrMainFeatureType(object, ignore = FALSE) <- value

vrMainFeatureType(object, ...) <- value

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. If NULL, the default assay will be used, see vrMainAssay. If given as "all", then provides a summary of spatial systems across all assays.
value

the name of main feature set.
ignore

ignore if some assays dont have the feature set name

vrMainImage

Description

Get the main image

Set the main image

Usage

vrMainImage(object, ...)

## S4 method for signature 'VoltRon'
vrMainImage(object, assay = NULL)

## S4 method for signature 'vrAssay'
vrMainImage(object)

## S4 method for signature 'vrAssayV2'
vrMainImage(object)

## S4 replacement method for signature 'VoltRon'
vrMainImage(object, assay = NULL) <- value

## S4 replacement method for signature 'vrAssay'
vrMainImage(object, ignore = FALSE) <- value

## S4 replacement method for signature 'vrAssayV2'
vrMainImage(object, ignore = FALSE) <- value

vrMainImage(object, ...) <- value

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. If NULL, the default assay will be used, see vrMainAssay. If given as "all", then provides a summary of spatial systems across all assays.
value

the name of main spatial coordinate system.
ignore

if TRUE, the non-existing spatial coordinate system will be ignored.

vrMainSpatial

Description

Get the main spatial system name

Set the main image

Usage

vrMainSpatial(object, ...)

## S4 method for signature 'VoltRon'
vrMainSpatial(object, assay = NULL)

## S4 method for signature 'vrAssay'
vrMainSpatial(object)

## S4 method for signature 'vrAssayV2'
vrMainSpatial(object)

## S4 replacement method for signature 'VoltRon'
vrMainSpatial(object, assay = NULL) <- value

## S4 replacement method for signature 'vrAssay'
vrMainSpatial(object, ignore = FALSE) <- value

## S4 replacement method for signature 'vrAssayV2'
vrMainSpatial(object, ignore = FALSE) <- value

vrMainSpatial(object, ...) <- value

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. If NULL, the default assay will be used, see vrMainAssay.
value

the name of main spatial coordinate system
ignore

if TRUE, the non-existing spatial coordinate system will be ignored.

The vrMetadata (VoltRon Metadata) Class

Description

The vrMetadata (VoltRon Metadata) Class

Slots

tile

the metadata of tiles

molecule

the metadata of molecules

cell

the metadata of cells

spot

the metadata of spot

ROI

the metadata of ROI

vrNeighbourhoodEnrichment

Description

Conduct Neighborhood enrichment test for pairs of clusters for all assays

Usage

vrNeighbourhoodEnrichment(
  object,
  assay = NULL,
  group.by = NULL,
  graph.type = "delaunay",
  num.sim = 1000,
  seed = 1,
  verbose = TRUE
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
group.by

a column from metadata to separate spatial points
graph.type

the type of graph to determine spatial neighborhood
num.sim

the number of simulations
seed

seed
verbose

verbose

vrNeighbourhoodEnrichmentPlot

Description

Plotting results of vrNeighbourhoodEnrichment

Usage

vrNeighbourhoodEnrichmentPlot(
  results,
  assay = NULL,
  type = c("assoc", "segreg")
)

Arguments

results

The results from vrNeighbourhoodEnrichment
assay

assay name (exp: Assay1), see SampleMetadata.
type

the type of spatial test. Either "assoc" for association test or "segreg" for segregation test

vrPercentagePlot

Description

vrPercentagePlot

Usage

vrProportionPlot(
  object,
  assay = NULL,
  x.label = NULL,
  split.by = NULL,
  split.method = "facet_wrap",
  ncol = 2,
  nrow = NULL
)

Arguments

object

a VoltRon object
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
x.label

labels of the x axis
split.by

the column to split the barplots by
split.method

either facet_grid or facet_wrap, not affected if split.by is NULL
ncol

column wise number of plots, for ggarrange
nrow

row wise number of plots, for ggarrange

The vrSample (VoltRon Sample) Class

Description

The vrSample (VoltRon Sample) Class

Slots

layer

A list of layers (vrLayer)

zlocation

a vector of z coordinates of layers

adjacency

an adjacency matrix of connected layers within a block

Methods for vrSample objects

Description

Methods for vrSample objects for generics defined in other packages

Usage

## S4 method for signature 'vrSample,character,ANY'
x[[i]]

## S4 replacement method for signature 'vrSample,character,ANY'
x[[i]] <- value

## S4 method for signature 'vrBlock,character,ANY'
x[[i]]

## S4 replacement method for signature 'vrBlock,character,ANY'
x[[i]] <- value

Arguments

x

A vrSample object
i

the name of layer associated with the sample, see SampleMetadata
value

a vrLayer object, see vrLayer

Functions

  • x[[i: Accessing vrLayer objects from vrSample objects

  • `[[`(x = vrSample, i = character, j = ANY) <- value: Accessing vrLayer objects from vrSample objects

  • x[[i: (deprecated) Accessing vrLayer objects from vrBlock objects

  • `[[`(x = vrBlock, i = character, j = ANY) <- value: (deprecated) Overwriting vrLayer objects from vrBlock objects

Get Sample names

Description

Given a vrMetadata object, give names of samples

Usage

vrSampleNames(object, ...)

## S4 method for signature 'vrMetadata'
vrSampleNames(object)

Arguments

object

a vrMetadata object.
...

arguments passed to other methods.

vrScatterPlot

Description

get a scatter plot between two features

Usage

vrScatterPlot(
  object,
  feature.1,
  feature.2,
  norm = TRUE,
  assay = NULL,
  pt.size = 2,
  font.size = 2,
  group.by = "label",
  label = FALSE,
  trend = FALSE
)

Arguments

object

a VoltRon object
feature.1

first feature
feature.2

second feature
norm

if TRUE, the normalize data will be used
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
pt.size

point size
font.size

font size
group.by

a column of metadata from Metadata used as grouping label for the spatial entities
label

whether labels are visualized or not
trend

inserting a trend line two the scatter plot

vrSegments

Description

Given a VoltRon, vrAssay or vrSpatial object, get and set the segment coordinates of assays and coordinate systems

Usage

vrSegments(object, ...)

## S4 method for signature 'VoltRon'
vrSegments(
  object,
  assay = NULL,
  image_name = NULL,
  spatial_name = NULL,
  reg = FALSE,
  as.data.frame = FALSE
)

## S4 method for signature 'vrAssay'
vrSegments(object, image_name = NULL, spatial_name = NULL, reg = FALSE)

## S4 method for signature 'vrAssayV2'
vrSegments(object, image_name = NULL, spatial_name = NULL, reg = FALSE)

## S4 method for signature 'vrImage'
vrSegments(object)

## S4 method for signature 'vrSpatial'
vrSegments(object)

## S4 replacement method for signature 'VoltRon'
vrSegments(object, image_name = NULL, spatial_name = NULL, reg = FALSE) <- value

## S4 replacement method for signature 'vrAssay'
vrSegments(object, image_name = NULL, spatial_name = NULL, reg = FALSE) <- value

## S4 replacement method for signature 'vrAssayV2'
vrSegments(object, image_name = NULL, spatial_name = NULL, reg = FALSE) <- value

## S4 replacement method for signature 'vrImage'
vrSegments(object) <- value

## S4 replacement method for signature 'vrSpatial'
vrSegments(object) <- value

vrSegments(object, ...) <- value

Arguments

object

a VoltRon, vrAssay or vrSpatial object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
image_name

(deprecated, use spatial_name) the name/key of the image associated with the coordinates
spatial_name

the name/key of the spatial system associated with the coordinates
reg

TRUE if registered coordinates of the main image (vrMainImage) is requested
as.data.frame

if TRUE, the coordinates of segment nodes will be returned as a data frame
value

segments

The vrSpatial (VoltRon Spatial) Class

Description

The vrSpatial (VoltRon Spatial) Class

Slots

coords

spatial coordinates of the assay

segments

spatial coordinates of the segments, if available

image

image of the spatial assay, bitmap class

main_channel

the key of the main channel of vrImage object

vrSpatialFeaturePlot

Description

Plotting single/multiple features of spatially resolved cells, spots, and ROI on associated images from multiple assays in a VoltRon object.

Usage

vrSpatialFeaturePlot(
  object,
  features,
  combine.features = FALSE,
  group.by = "label",
  plot.segments = FALSE,
  n.tile = NULL,
  norm = TRUE,
  log = FALSE,
  assay = NULL,
  graph.name = NULL,
  ncol = 2,
  nrow = NULL,
  font.size = 2,
  pt.size = 2,
  cell.shape = 16,
  title.size = 10,
  alpha = 0.6,
  keep.scale = "feature",
  label = FALSE,
  spatial = NULL,
  channel = NULL,
  background.color = NULL,
  background = NULL,
  reg = FALSE,
  crop = FALSE,
  scale.image = TRUE,
  common.legend = FALSE,
  legend.loc = "right",
  collapse.plots = TRUE
)

Arguments

object

a VoltRon object
features

a set of features to be visualized, either from vrFeatures of raw or normalized data or columns of the Metadata.
combine.features

whether to combine all features in one plot
group.by

a column of metadata from Metadata used as grouping label for the spatial entities
plot.segments

plot segments from vrSegments instead of points
n.tile

The number of tiles on x-and y-axis for rasterizing points (see geom_tile). The rasterization is performed automatically for large number of points Only applicable to spots, cells and molecules. If n.tile = 0 will turn of automated rasterization.
norm

if TRUE, the normalized data is used
log

if TRUE, data features (excluding metadata features) will be log transformed
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
graph.name

if not NULL, the spatial graph is with name graph.name is visualized as well, see vrGraphNames
ncol

column wise number of plots, for ggarrange
nrow

row wise number of plots, for ggarrange
font.size

font size
pt.size

point size
cell.shape

the shape of the points representing cells, see geom_point
title.size

title size of legend and plot
alpha

alpha level of colors of visualized points and segments
keep.scale

whether unify all scales for all features or not
label

if TRUE, labels of ROIs will be visualized too
spatial

the name of the main spatial system
channel

the name of the channel associated with the image
background.color

the color of plot background if a channel is not specified, or the spatial coord system doesnt have an image.
background

(DEPRECATED) the background of the plot. Either an image name, see vrImageNames or a vector of length two with image name and a channel name, see vrImageChannelNames. Type "black" or "white" for black or white backgrounds. if NULL, the main image (vrMainSpatial) and main channel (vrMainChannel) will be in the background. Otherwise the background will be grey.
reg

TRUE if registered coordinates of the main image (vrMainSpatial) is requested
crop

whether to crop an image of a spot assay to the extend of spots
scale.image

if TRUE, background image will be scaled down to a low resolution (width: 1000px)
common.legend

whether to use a common legend for all plots, see ggarrange
legend.loc

the location of the legend, default is "right"
collapse.plots

whether to combine all ggplots

vrSpatialNames

Description

Get names of all spatial systems

Usage

vrSpatialNames(object, ...)

## S4 method for signature 'VoltRon'
vrSpatialNames(object, assay = NULL)

## S4 method for signature 'vrAssay'
vrSpatialNames(object)

## S4 method for signature 'vrAssayV2'
vrSpatialNames(object)

Arguments

object

a VoltRon or vrAssay object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay. If equals to "all", then provides a summary of spatial systems across all assays

vrSpatialPlot

Description

Plotting identification of spatially resolved cells, spots, and ROI on associated images from multiple assays in a VoltRon object.

Usage

vrSpatialPlot(
  object,
  group.by = "Sample",
  plot.segments = FALSE,
  group.ids = NULL,
  colors = NULL,
  n.tile = NULL,
  assay = NULL,
  graph.name = NULL,
  graph.edge.color = "orange",
  reduction = NULL,
  ncol = 2,
  nrow = NULL,
  font.size = 2,
  pt.size = 2,
  cell.shape = 21,
  alpha = 1,
  label = FALSE,
  spatial = NULL,
  channel = NULL,
  background.color = NULL,
  background = NULL,
  reg = FALSE,
  crop = FALSE,
  combine.groups = FALSE,
  legend.pt.size = 2,
  legend.text.size = 14,
  scale.image = TRUE,
  legend.loc = "right",
  common.legend = TRUE,
  collapse.plots = TRUE,
  interactive = FALSE,
  shiny.options = list()
)

Arguments

object

a VoltRon object
group.by

a column of metadata from Metadata used as grouping label for the spatial entities
plot.segments

plot segments from vrSegments instead of points
group.ids

a subset of categories defined in metadata column from group.by
colors

the color set for group.by. Should be of the same size of group.id (if specified) or unique elements in group.by
n.tile

The number of tiles on x-and y-axis for rasterizing points (see geom_tile). The rasterization is performed automatically for large number of points Only applicable to spots, cells and molecules. If n.tile = 0 will turn of automated rasterization.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
graph.name

if not NULL, the spatial graph is with name graph.name is visualized as well, see vrGraphNames
graph.edge.color

the colors of the graph edges, if graph.name is not NULL.
reduction

used by vrSpatialPlotVitessce to visualize an embedding alongside with the spatial plot.
ncol

column wise number of plots, for ggarrange
nrow

row wise number of plots, for ggarrange
font.size

font size
pt.size

point size
cell.shape

the shape of the points representing cells, see geom_point
alpha

alpha level of colors of visualized points and segments
label

if TRUE, the labels of the ROI assays will be visualized
spatial

the name of the main spatial system
channel

the name of the channel associated with the image
background.color

the color of plot background if a channel is not specified, or the spatial coord system doesnt have an image.
background

(DEPRECATED) the background of the plot. Either an image name, see vrImageNames or a vector of length two with image name and a channel name, see vrImageChannelNames. Type "black" or "white" for black or white backgrounds. if NULL, the main image (vrMainSpatial) and main channel (vrMainChannel) will be in the background. Otherwise the background will be grey.
reg

TRUE if registered coordinates of the main image (vrMainSpatial) is requested
crop

whether to crop an image of a spot assay to the extend of spots
combine.groups

if TRUE, tile colors will reflect relative abundance of either of two groups, strictly for visualizing two groups when assay is a molecule typed and tiled (see n.tile).
legend.pt.size

the size of points at the legend
legend.text.size

the size of the text at the legend
scale.image

if TRUE, background image will be scaled down to a low resolution (width: 1000px)
legend.loc

the location of the legend, default is "right"
common.legend

whether to use a common legend for all plots, see ggarrange
collapse.plots

whether to combine all ggplots
interactive

if TRUE, run interactive plot
shiny.options

a list of shiny options (browser, host, port etc.) passed options arguement of shinyApp. For more information, see runApp

vrSpatialPoints

Description

Get and set spatial entities.

Usage

vrSpatialPoints(object, ...)

## S4 method for signature 'VoltRon'
vrSpatialPoints(object, assay = NULL)

## S4 method for signature 'vrMetadata'
vrSpatialPoints(object, assay = NULL)

## S4 method for signature 'vrAssay'
vrSpatialPoints(object)

## S4 method for signature 'vrAssayV2'
vrSpatialPoints(object)

## S4 method for signature 'vrImage'
vrSpatialPoints(object)

## S4 method for signature 'vrSpatial'
vrSpatialPoints(object)

## S4 method for signature 'vrSample'
vrSpatialPoints(object)

## S4 method for signature 'vrBlock'
vrSpatialPoints(object)

## S4 method for signature 'vrLayer'
vrSpatialPoints(object)

## S4 replacement method for signature 'vrAssay'
vrSpatialPoints(object) <- value

## S4 replacement method for signature 'vrAssayV2'
vrSpatialPoints(object) <- value

## S4 replacement method for signature 'vrImage'
vrSpatialPoints(object) <- value

## S4 replacement method for signature 'vrSpatial'
vrSpatialPoints(object) <- value

vrSpatialPoints(object, ...) <- value

Arguments

object

a VoltRon, vrSample, vrLayer, vrAssay or vrSpatial object.
...

arguments passed to other methods.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
value

names for spatial points

Examples

vrSpatialPoints(visium_data)
vrSpatialPoints(visium_data, assay = "Visium")
vrSpatialPoints(visium_data, assay = "Assay1")

vrViolinPlot

Description

vrViolinPlot

Usage

vrViolinPlot(
  object,
  features = NULL,
  assay = NULL,
  group.by = "Sample",
  norm = TRUE,
  pt.size = 0.5,
  plot.points = TRUE,
  ncol = 2,
  nrow = NULL
)

Arguments

object

a VoltRon object
features

a set of features to be visualized, either from vrFeatures of raw or normalized data or columns of the Metadata.
assay

assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see SampleMetadata. if NULL, the default assay will be used, see vrMainAssay.
group.by

a column of metadata from Metadata used as grouping label for the spatial entities
norm

if TRUE, the normalized data is used
pt.size

point size
plot.points

if TRUE, measures are visualized as points as well.
ncol

column wise number of plots, for ggarrange
nrow

row wise number of plots, for ggarrange

warpImage

Description

Warping a query image given a homography image

Usage

warpImage(ref_image, query_image, mapping)

Arguments

ref_image

reference image
query_image

query image
mapping

a list of the homography matrices and TPS keypoints

getRcppWarpImage

Description

Warping a query image given a homography image

Usage

warpSimpleITKImage(ref_image, query_image, mapping)

Arguments

ref_image

reference image
query_image

query image
mapping

a list of the homography matrices and TPS keypoints

Example Xenium Data

Description

This VoltRon object is used for testing and as an example

Usage

xenium_data

Format

An object of class VoltRon of length 1.

Source

Created to serve as an example.

Examples

data(xenium_data)

zarrcreateGroup

Description

get information of an ImageArray object

Usage

zarrcreateGroup(store, name)

Arguments

store

the location of (zarr) store
name

name of the group