swh:1:snp:0da231f3ffdb3226650880f1b61d5d5cdcbd749b
Tip revision: 656fc8b562d53e5d0cedda9e09d9dda81e8c00e9 authored by David Collins on 29 February 2024, 13:44:33 UTC
Merge pull request #8550 from satijalab/develop
Merge pull request #8550 from satijalab/develop
Tip revision: 656fc8b
ReadVitessce.Rd
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/preprocessing.R, R/convenience.R
\name{ReadVitessce}
\alias{ReadVitessce}
\alias{LoadHuBMAPCODEX}
\title{Read Data From Vitessce}
\usage{
ReadVitessce(
counts = NULL,
coords = NULL,
molecules = NULL,
type = c("segmentations", "centroids"),
filter = NA_character_
)
LoadHuBMAPCODEX(data.dir, fov, assay = "CODEX")
}
\arguments{
\item{counts}{Path or URL to a Vitessce-formatted JSON file with
expression data; should end in \dQuote{\code{.genes.json}} or
\dQuote{\code{.clusters.json}}; pass \code{NULL} to skip}
\item{coords}{Path or URL to a Vitessce-formatted JSON file with cell/spot
spatial coordinates; should end in \dQuote{\code{.cells.json}};
pass \code{NULL} to skip}
\item{molecules}{Path or URL to a Vitessce-formatted JSON file with molecule
spatial coordinates; should end in \dQuote{\code{.molecules.json}};
pass \code{NULL} to skip}
\item{type}{Type of cell/spot spatial coordinates to return,
choose one or more from:
\itemize{
\item \dQuote{segmentations} cell/spot segmentations
\item \dQuote{centroids} cell/spot centroids
}}
\item{filter}{A character to filter molecules by, pass \code{NA} to skip
molecule filtering}
\item{data.dir}{Path to a directory containing Vitessce cells
and clusters JSONs}
\item{fov}{Name to store FOV as}
\item{assay}{Name to store expression matrix as}
}
\value{
\code{ReadVitessce}: A list with some combination of the
following values:
\itemize{
\item \dQuote{\code{counts}}: if \code{counts} is not \code{NULL}, an
expression matrix with cells as columns and features as rows
\item \dQuote{\code{centroids}}: if \code{coords} is not \code{NULL} and
\code{type} is contains\dQuote{centroids}, a data frame with cell centroids
in three columns: \dQuote{x}, \dQuote{y}, and \dQuote{cell}
\item \dQuote{\code{segmentations}}: if \code{coords} is not \code{NULL} and
\code{type} contains \dQuote{centroids}, a data frame with cell
segmentations in three columns: \dQuote{x}, \dQuote{y} and \dQuote{cell}
\item \dQuote{\code{molecules}}: if \code{molecules} is not \code{NULL}, a
data frame with molecule spatial coordinates in three columns: \dQuote{x},
\dQuote{y}, and \dQuote{gene}
}
\code{LoadHuBMAPCODEX}: A \code{\link[SeuratObject]{Seurat}} object
}
\description{
Read in data from Vitessce-formatted JSON files
}
\note{
This function requires the
\href{https://cran.r-project.org/package=jsonlite}{\pkg{jsonlite}} package
to be installed
}
\section{Progress Updates with \pkg{progressr}}{
This function uses
\href{https://cran.r-project.org/package=progressr}{\pkg{progressr}} to
render status updates and progress bars. To enable progress updates, wrap
the function call in \code{\link[progressr]{with_progress}} or run
\code{\link[progressr:handlers]{handlers(global = TRUE)}} before running
this function. For more details about \pkg{progressr}, please read
\href{https://progressr.futureverse.org/articles/progressr-intro.html}{\code{vignette("progressr-intro")}}
}
\examples{
\dontrun{
coords <- ReadVitessce(
counts =
"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.genes.json",
coords =
"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.cells.json",
molecules =
"https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.molecules.json"
)
names(coords)
coords$counts[1:10, 1:10]
head(coords$centroids)
head(coords$segmentations)
head(coords$molecules)
}
}
\concept{preprocessing}