Package 'xenLite'

Title: Simple classes and methods for managing Xenium datasets
Description: Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.
Authors: Vincent Carey [aut, cre]
Maintainer: Vincent Carey <[email protected]>
License: Artistic-2.0
Version: 1.1.0
Built: 2024-10-31 06:40:09 UTC
Source: https://github.com/bioc/xenLite

Help Index

formal bracket definition, that leaves parquet geometry information alone.

Description

formal bracket definition, that leaves parquet geometry information alone.

Usage

## S4 method for signature 'XenSPEP,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

Arguments

x

instance of XenSPEP
i

feature selection
j

cell selection
...

passed to SpatialExperiment methods
drop

logical(1)

Value

XenSPEP instance

Note

Gives a message and calls callNextMethod.

cache and/or retrieve path to an ome.tif file for demonstration

Description

cache and/or retrieve path to an ome.tif file for demonstration

Usage

cacheMtif(
  cache = BiocFileCache::BiocFileCache(),
  url =
    "https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/morphology_focus_0001.ome.tif"
)

Arguments

cache

defaults to BiocFileCache::BiocFileCache()
url

location where tiff file can be retrieved

Value

path to cached resource

Note

The tiff file was retrieved after running SFEData::XeniumOutput("v2"), and depicts a pancreas tissue sample.

Examples

pa <- cacheMtif()
if (!requireNamespace("tiff")) stop("install tiff package to run this example")
x <- tiff::readTIFF(pa)
plot(0, xlim = c(0, 1000), ylim = c(0, 1000), xlab = " ", ylab = " ")
rasterImage(x * 5.5, 0, 0, 1000, 1000)

cache and/or retrieve path to an SFE of V1 lung demo data from 10x

Description

cache and/or retrieve path to an SFE of V1 lung demo data from 10x

Usage

cacheSfeLungNtx(
  cache = BiocFileCache::BiocFileCache(),
  url = "https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/sfeLung.zip"
)

Arguments

cache

defaults to BiocFileCache::BiocFileCache()
url

location where zip file can be retrieved

Value

path to cached resource

Note

Lacks transcript coordinates

cache and/or retrieve path to Xenium Lung Adenocarcinoma example data, zipped SPEP accompanied by parquet

Description

cache and/or retrieve path to Xenium Lung Adenocarcinoma example data, zipped SPEP accompanied by parquet

Usage

cacheXenLuad(
  cache = BiocFileCache::BiocFileCache(),
  url = "https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/luad_lite.zip"
)

Arguments

cache

defaults to BiocFileCache::BiocFileCache()
url

location where zip file can be retrieved

Value

path to cached resource

Examples

if (interactive()) {
  pa <- cacheXenLuad()
  luad <- restoreZipXenSPEP(pa)
  print(luad)
  print(slot(luad, "cellbounds_path"))
  viewSeg(luad, xlim = c(4000, 4500), ylim = c(2000, 2500))
}

counts-in-memory version of melanoma 5k dataset

Description

counts-in-memory version of melanoma 5k dataset

Usage

cacheXenPdmelLite(
  cache = BiocFileCache::BiocFileCache(),
  url = "https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/pdmel_lite.zip"
)

Arguments

cache

defaults to BiocFileCache::BiocFileCache()
url

location where zip file can be retrieved

Value

path to cached resource

Examples

if (interactive()) {
  pa <- cacheXenPdmelLite()
  pdmel_lite <- restoreZipXenSPEP(pa)
  print(pdmel_lite)
}

counts-in-memory version of prostate 5k dataset

Description

counts-in-memory version of prostate 5k dataset

Usage

cacheXenProstLite(
  cache = BiocFileCache::BiocFileCache(),
  url = "https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/prost_lite.zip"
)

Arguments

cache

defaults to BiocFileCache::BiocFileCache()
url

location where zip file can be retrieved

Value

path to cached resource

Examples

if (interactive()) {
  pa <- cacheXenProstLite()
  prost_lite <- restoreZipXenSPEP(pa)
  print(prost_lite)
}

restrict XenSPEP to cells with centroids in specified rectangle, also restrict boundary and transcript location features

Description

restrict XenSPEP to cells with centroids in specified rectangle, also restrict boundary and transcript location features

Usage

clipRect(xsce, xlim, ylim)

Arguments

xsce

XenSPEP instance
xlim

numeric(2)
ylim

numeric(2)

Value

XenSPEP instance

Note

Could be too RAM-hungry.

Examples

args(clipRect)

simple app to explore an image

Description

simple app to explore an image

Usage

demoapp(simple = FALSE)

Arguments

simple

logical(1) if TRUE, use a cached tiff for illustration

Value

No value returned, run for side effect of app initiation.

Note

Navigate file input control to location of tiffs

Examples

if (interactive()) demoapp(simple = TRUE)

helper function to map ENS ids to symbols

Description

helper function to map ENS ids to symbols

Usage

e2sym(x)

Arguments

x

character() mix of Ensembl Ids and other strings; the latter are left unchanged

Value

a vector like x with gene symbols from v79 mapping substituted where possible

Examples

e2sym(c("ABC", "ENSG00000213088", "ENSG00000107796", "ENSG00000163017"))

mapping from ENSG to symbols based on EnsDb.Hsapiens.v79

Description

mapping from ENSG to symbols based on EnsDb.Hsapiens.v79

Usage

e79sym

Format

character()

Value

character vector

Note

named character vector with values gene symbols, name ENSG ids

Examples

data(e79sym)
head(e79sym)

method for cell boundary extraction

Description

method for cell boundary extraction

Usage

getCellBoundaries(x)

Arguments

x

instance of XenSPEP

Value

reference to ingested parquet

Examples

showMethods("getCellBoundaries")

method for cell boundary extraction

Description

method for cell boundary extraction

Usage

## S4 method for signature 'XenSPEP'
getCellBoundaries(x)

Arguments

x

instance of XenSPEP

Value

reference to ingested parquet

method for nucleus boundary extraction

Description

method for nucleus boundary extraction

Usage

getNucleusBoundaries(x)

Arguments

x

instance of XenSPEP

Value

reference to ingested parquet

Examples

showMethods("getNucleusBoundaries")

method for nucleus boundary extraction

Description

method for nucleus boundary extraction

Usage

## S4 method for signature 'XenSPEP'
getNucleusBoundaries(x)

Arguments

x

instance of XenSPEP

Value

reference to ingested parquet

method for transcript extraction

Description

method for transcript extraction

Usage

getTranscripts(x)

Arguments

x

instance of XenSPEP

Value

reference to ingested parquet

Examples

showMethods("getTranscripts")

method for transcript extraction

Description

method for transcript extraction

Usage

## S4 method for signature 'XenSPEP'
getTranscripts(x)

Arguments

x

instance of XenSPEP

Value

reference to ingested parquet

Examples

showMethods("getTranscripts")

prepare a XenSPEP for ggplot2 visualization

Description

prepare a XenSPEP for ggplot2 visualization

Usage

ggprepSeg(xsce, xlim = c(5800, 6200), ylim = c(6300, 6700))

Arguments

xsce

XenSPEP instance
xlim

numeric(2)
ylim

numeric(2)

Value

a list with components 'bounds' (data.frame including relevant colData rows (all colData variables) and cell boundary coordinates) and 'txdata', a filtered arrow Table.

Note

This is idiosyncratic. Quintiles of cell_area (values in 'sizq') are produced, and transcript locations are filtered. A more general approach that allows selection of coloring of cells by feature characteristics is needed.

Examples

pa <- cacheXenLuad()
luad <- restoreZipXenSPEP(pa)
hh <- ggprepSeg(luad, c(4000, 4500), c(2000, 2500))
ggplot2::ggplot(hh$bounds, ggplot2::aes(
  x = vertex_x, y = vertex_y, group = cell_id,
  colour = sizq, fill = sizq
)) +
  ggplot2::geom_polygon(alpha = .5)

produce a pre-loaded XenSPEP (SpatialExperiment with parquet references)

Description

produce a pre-loaded XenSPEP (SpatialExperiment with parquet references)

Usage

ingest_xen(folder)

Arguments

folder

character(1) 'standard' Xenium output folder

Value

instance of XenSPEP

Examples

chkns <- function(pkstring) {
  if (!requireNamespace(pkstring)) {
    message(sprintf("install %s to use this feature; returning NULL", pkstring))
    return(NULL)
  }
}
chkns("SFEData")
chkns("HDF5Array")
chkns("SingleCellExperiment")
if (requireNamespace("SFEData")) {
  td <- tempdir()
  z <- SFEData::XeniumOutput("v2", td)
  ii <- ingest_xen(file.path(td, "xenium2"))
  print(validObject(ii))
  plot(SpatialExperiment::spatialCoords(ii), pch = ".")
}

read and bind parquet data to XenSPEP

Description

read and bind parquet data to XenSPEP

Usage

loadGeometry(x)

Arguments

x

instance of XenSPEP

Value

instance of XenSPEP

read and bind parquet data to XenSPEP

Description

read and bind parquet data to XenSPEP

Usage

## S4 method for signature 'XenSPEP'
loadGeometry(x)

Arguments

x

instance of XenSPEP

Value

instance of XenSPEP

plot method for ggplot2-prepared XenSPEP

Description

plot method for ggplot2-prepared XenSPEP

Usage

plotXenGgprep(x, y, ...)

Arguments

x

instance of S3 class 'xen_ggprep'
y

not used
...

not used

Value

ggplot

Note

roxygen had problems with this

Examples

pa <- cacheXenLuad()
luad <- restoreZipXenSPEP(pa)
hh <- ggprepSeg(luad, c(4000, 4500), c(2000, 2500))
plotXenGgprep(hh)

print method for ggplot2-prepared XenSPEP

Description

print method for ggplot2-prepared XenSPEP

Usage

printXenGgprep(x, ...)

Arguments

x

instance of S3 class 'xen_ggprep'
...

not used

Value

operates with cat()

utility for dealing with cached Xen_SPEP in temp folder

Description

utility for dealing with cached Xen_SPEP in temp folder

Usage

resetParqPaths(xsp, base)

Arguments

xsp

instance of XenSPEP
base

folder path where parquet files are found

Value

XenSPEP instance

Note

Will prepend current folder path to parquet-oriented slot values.

use unzip, readRDS, and loadGeometry to restore a XenSPEP

Description

use unzip, readRDS, and loadGeometry to restore a XenSPEP

Usage

restoreZipXenSPEP(zipf, exdir = tempdir())

Arguments

zipf

character(1) path to zip file created with 'zipXenSPEP'
exdir

character(1) defaults to tempdir(), where contents are unpacked

Value

instance of XenSPEP

Note

Session folder position will change with setwd(), on.exit ensures return to position when started.

Examples

# used implicitly
if (interactive()) {
  example(cacheXenLuad)
}

display aspects of XenSPEP

Description

display aspects of XenSPEP

Usage

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

Arguments

object

instance of XenSPEP

Value

operates with cat()

naive polygon viewer

Description

naive polygon viewer

Usage

viewSeg(x, xlim, ylim, show_tx = FALSE, ...)

Arguments

x

instance of XenSPEP
xlim

numeric(2) ordered vector of max and min on x
ylim

numeric(2) ordered vector of max and min on y
show_tx

logical(1) display transcript locations if TRUE, defaults to FALSE.
...

passed to polygon()

Value

run for side effect of plotting

Note

This is more RAM-sparing than clipRect followed by view.

Examples

luad <- cacheXenLuad()
pa <- cacheXenLuad()
luad <- restoreZipXenSPEP(pa)
rownames(luad) <- make.names(SummarizedExperiment:::rowData(luad)$Symbol, unique = TRUE)
out <- viewSeg(luad, c(5800, 6300), c(1300, 1800), lwd = .5)
out$ncells

naive polygon viewer, will indicate presence of transcripts for two genes in cells

Description

naive polygon viewer, will indicate presence of transcripts for two genes in cells

Usage

viewSegG2(x, xlim, ylim, gene1, gene2, show_tx = FALSE, ...)

Arguments

x

instance of XenSPEP
xlim

numeric(2) ordered vector of max and min on x
ylim

numeric(2) ordered vector of max and min on y
gene1

character(1) gene to be checked, cell polygon will be filled if gene has non-zero count
gene2

character(1) gene to be checked, cell polygon will be filled if gene has non-zero count
show_tx

logical(1) display transcript locations if TRUE, defaults to FALSE.
...

passed to polygon()

Value

Primarily for plotting. A list is invisibly returned with elements polys, ncells and call.

Note

This is more RAM-sparing than clipRect followed by view. Colors are pre-assigned for individual and joint occupancies in this draft of this visualizer.

Examples

luad <- cacheXenLuad()
pa <- cacheXenLuad()
luad <- restoreZipXenSPEP(pa)
rownames(luad) <- make.names(SummarizedExperiment:::rowData(luad)$Symbol, unique = TRUE)
out <- viewSegG2(luad, c(5800, 6300), c(1300, 1800), lwd = .5, gene1 = "CD4", gene2 = "EPCAM")
legend(5800, 1370, fill = c("purple", "cyan", "pink"), legend = c("CD4", "EPCAM", "both"))
out$ncells

XenSPEP (SpatialExperiment with parquet references) constructor

Description

XenSPEP (SpatialExperiment with parquet references) constructor

Usage

XenSPEP(folder)

Arguments

folder

character(1) 'standard' Xenium output folder

Value

instance of XenSPEP

Examples

# is not used yet
args(XenSPEP)

manage SpatialExperiment with parquet references

Description

manage SpatialExperiment with parquet references

serialize the collection of XenSPEP and parquet with zip

Description

serialize the collection of XenSPEP and parquet with zip

Usage

zipXenSPEP(xsp, targetfile)

Arguments

xsp

instance of XenSPEP with geometry loaded
targetfile

character(1) destination of zip process

Value

output of zip()

Note

a .rds and three parquet files are zipped together for restoration by 'restoreZipXenSPEP'. The outcome is 'paste0(targetfile, ".zip")'.

Examples

zipXenSPEP