|
a |
|
b/man/subset.Rd |
|
|
1 |
% Generated by roxygen2: do not edit by hand |
|
|
2 |
% Please edit documentation in R/objects.R |
|
|
3 |
\name{subset,VoltRon-method} |
|
|
4 |
\alias{subset,VoltRon-method} |
|
|
5 |
\alias{subset} |
|
|
6 |
\title{Subsetting VoltRon objects} |
|
|
7 |
\usage{ |
|
|
8 |
\S4method{subset}{VoltRon}( |
|
|
9 |
x, |
|
|
10 |
subset, |
|
|
11 |
samples = NULL, |
|
|
12 |
assays = NULL, |
|
|
13 |
spatialpoints = NULL, |
|
|
14 |
features = NULL, |
|
|
15 |
image = NULL, |
|
|
16 |
interactive = FALSE, |
|
|
17 |
use.points.only = FALSE, |
|
|
18 |
shiny.options = list(launch.browser = getOption("shiny.launch.browser", interactive())) |
|
|
19 |
) |
|
|
20 |
} |
|
|
21 |
\arguments{ |
|
|
22 |
\item{x}{a VoltRon object} |
|
|
23 |
|
|
|
24 |
\item{subset}{Logical statement for subsetting} |
|
|
25 |
|
|
|
26 |
\item{samples}{the set of samples to subset the object} |
|
|
27 |
|
|
|
28 |
\item{assays}{the set of assays to subset the object} |
|
|
29 |
|
|
|
30 |
\item{spatialpoints}{the set of spatial points to subset the object} |
|
|
31 |
|
|
|
32 |
\item{features}{the set of features to subset the object} |
|
|
33 |
|
|
|
34 |
\item{image}{the subseting string passed to \link{image_crop}} |
|
|
35 |
|
|
|
36 |
\item{interactive}{TRUE if interactive subsetting on the image is demanded} |
|
|
37 |
|
|
|
38 |
\item{use.points.only}{if \code{interactive} is \code{TRUE}, use spatial points instead of the reference image} |
|
|
39 |
|
|
|
40 |
\item{shiny.options}{a list of shiny options (launch.browser, host, port etc.) passed \code{options} arguement of \link{shinyApp}. For more information, see \link{runApp}} |
|
|
41 |
} |
|
|
42 |
\description{ |
|
|
43 |
Given a VoltRon object, subset the object given one of the attributes |
|
|
44 |
} |
|
|
45 |
\examples{ |
|
|
46 |
# example data |
|
|
47 |
data("visium_data") |
|
|
48 |
|
|
|
49 |
# subset based on assay |
|
|
50 |
subset(visium_data, assays = "Assay1") |
|
|
51 |
subset(visium_data, assays = "Visium") |
|
|
52 |
|
|
|
53 |
# subset based on samples |
|
|
54 |
subset(visium_data, samples = "Anterior1") |
|
|
55 |
|
|
|
56 |
# subset based on assay |
|
|
57 |
subset(visium_data, spatialpoints = c("GTTATATTATCTCCCT-1_Assay1", "GTTTGGGTTTCGCCCG-1_Assay1")) |
|
|
58 |
|
|
|
59 |
# subset based on features |
|
|
60 |
subset(visium_data, features = c("Map3k19", "Rab3gap1")) |
|
|
61 |
|
|
|
62 |
# interactive subsetting |
|
|
63 |
\dontrun{ |
|
|
64 |
visium_subset_data <- subset(visium_data, interactive = TRUE) |
|
|
65 |
visium_subset <- visium_subset_data$subsets[[1]] |
|
|
66 |
} |
|
|
67 |
} |