-
Notifications
You must be signed in to change notification settings - Fork 0
/
.Rhistory
77 lines (77 loc) · 2.24 KB
/
.Rhistory
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
renv::activate()
renv::init()
renv::install("SpatialFeatureExperiment")
renv::install("SpatialFeatureExperiment")
renv::install("SpatialFeatureExperiment")
packageurl <- "https://cran.r-project.org/src/contrib/Archive/rgdal/rgdal_1.6-3.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
install.packages(packageurl, repos=NULL, type="source")
renv::install("SpatialFeatureExperiment")
install.packages(packageurl, repos=NULL, type="source")
renv::install("rgdal")
install.packages("rgdal")
install.packages("rgdal", dependencies = TRUE)
install.packages(packageurl, repos=NULL, type="source")
renv::install("SpatialExperiment")
library(SpatialExperiment)
example("read10xVisium", echo=FALSE)
renv::install("DropletUtils")
example("read10xVisium", echo=FALSE)
spe
head(spatialCoords(spe))
spatialCoordsNames(spe)
imgData(spe)
(spi) <- getImg(spe)
(spi) <- getImg(spe))
(spi <- getImg(spe))
identical(spi, imgData(spe)$data[[1]])
plot(imgRaster(spe))
plot(imgRaster(spe))
plot(img)
url <- "https://i.redd.it/3pw5uah7xo041.jpg"
spe <- addImg(spe,
sample_id = "section1",
image_id = "pomeranian",
imageSource = url,
scaleFactor = NA_real_,
load = TRUE)
img <- imgRaster(spe,
sample_id = "section1",
image_id = "pomeranian")
plot(img)
sessionInfo()
#| echo: false
#| output: false
#| warning: true
library(SpatialExperiment)
#| echo: false
#| output: false
#| warning: true
library(SpatialExperiment, quietly = TRUE)
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpatialFeatureExperiment")
renv::install(bioc::SpatialFeatureExperiment)
renv::install("bioc::SpatialFeatureExperiment")
renv::install("bioc::SpatialFeatureExperiment")
library(remotes)
renv::install(remotes)
renv::install("remotes")
library(remotes)
install_github("r-spatial/sf")
renv::install("rgdal")
install.packages("rgdal", repos = "http://cran.us.r-project.org", type = "source")
install.packages("rgdal2", repos = "http://cran.us.r-project.org", type = "source")
install.packages("sf2")
install.packages("sf")
install.packages("sf")
install.packages("rgdal")
install.packages("sf")
install.packages("sf")
install.packages("sf")
library("devtools")
install.packages("devtools")
devtools::install_github("r-spatial/sf")
sessionInfo()
library("r-sf")
library("sf")