The SpatialExperiment package provides classes and methods for single cell spatial data handling.
This vignettes shows how to create a SpatialExperiment class by loading a seqFISH spatial dataset.
The seqFISH data are part of the BIRS Biointegration Workshop Hackathon previously published in Zhu et al. 2018.
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpatialExperiment")We stored the provided seqFish and scRNA-seq data inside the SpatialExperiment external data seqFISH folder.
library(SpatialExperiment)fishCoordFile <- system.file(file.path("extdata", "seqFISH",
"fcortex.coordinates.txt"),
package="SpatialExperiment")
fishCoordinates <- read.table(fishCoordFile, header=FALSE, sep=" ")
colnames(fishCoordinates) <- c("Cell_ID", "Irrelevant", "x", "y")
fishCellLabsFile <- system.file(file.path("extdata", "seqFISH",
"seqfish_cell_labels.tsv"),
package="SpatialExperiment")
fishCellLabels <- read.table(file=fishCellLabsFile, header=FALSE, sep="\t")
colnames(fishCellLabels) <- c("Cell_ID", "cluster", "class", "classID",
"Irrelevant", "Prob")
fishFeatCountsFile <- system.file(file.path("extdata", "seqFISH",
"seqfish_normalized_cortex_b2_testing.txt"),
package="SpatialExperiment")
fishFeaturesCounts <- read.table(file=fishFeatCountsFile,
header=FALSE, sep="\t", row.names=1)We can load the data inside the SpatialExperiment class. We then use the show method for looking at the class description.
se <- SpatialExperiment(rowData=rownames(fishFeaturesCounts),
colData=fishCellLabels,
assays=SimpleList(counts=as.matrix(fishFeaturesCounts)),
spatialCoords=fishCoordinates)
show(se)## class: SpatialExperiment
## dim: 113 1597
## metadata(0):
## assays(1): counts
## rownames(113): abca15 abca9 ... zfp715 zfp90
## rowData names(1): X
## colnames(1597): V2 V3 ... V1597 V1598
## colData names(6): Cell_ID cluster ... Irrelevant Prob
## reducedDimNames(0):
## altExpNames(0):
## spatialCoordinates(4): Cell_ID Irrelevant x yWith the aid of the spatialCoords methods we can get and set the spatial coordinates.
spatialCoords(se)## DataFrame with 1597 rows and 4 columns
## Cell_ID Irrelevant x y
## <integer> <integer> <numeric> <numeric>
## 1 1 100 265.76 -231.14
## 2 2 100 290.48 -261.52
## 3 3 100 257.12 -133.35
## 4 4 100 753.46 -261.14
## 5 5 100 700.01 -169.05
## ... ... ... ... ...
## 1593 1593 100 1129.06 -1669.57
## 1594 1594 100 1044.02 -1872.66
## 1595 1595 100 1388.76 -1880.47
## 1596 1596 100 5172.85 -1340.96
## 1597 1597 100 5220.60 -1523.37We create a fake fish coordinates data frame and overwrite the old one, showing that the y coordinates are identical to the x ones.
fakeFishCoords <- cbind(fishCoordinates[,c(1:3)], fishCoordinates[,3])
colnames(fakeFishCoords) <- c("Cell_ID", "Irrelevant", "x", "y")
spatialCoords(se) <- fakeFishCoords
spatialCoords(se)## DataFrame with 1597 rows and 4 columns
## Cell_ID Irrelevant x y
## <integer> <integer> <numeric> <numeric>
## 1 1 100 265.76 265.76
## 2 2 100 290.48 290.48
## 3 3 100 257.12 257.12
## 4 4 100 753.46 753.46
## 5 5 100 700.01 700.01
## ... ... ... ... ...
## 1593 1593 100 1129.06 1129.06
## 1594 1594 100 1044.02 1044.02
## 1595 1595 100 1388.76 1388.76
## 1596 1596 100 5172.85 5172.85
## 1597 1597 100 5220.60 5220.60sessionInfo()## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.12-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.12-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] rjson_0.2.20 Matrix_1.2-18
## [3] SpatialExperiment_1.0.0 SingleCellExperiment_1.12.0
## [5] SummarizedExperiment_1.20.0 Biobase_2.50.0
## [7] GenomicRanges_1.42.0 GenomeInfoDb_1.26.0
## [9] IRanges_2.24.0 S4Vectors_0.28.0
## [11] BiocGenerics_0.36.0 MatrixGenerics_1.2.0
## [13] matrixStats_0.57.0 BiocStyle_2.18.0
##
## loaded via a namespace (and not attached):
## [1] knitr_1.30 XVector_0.30.0 magrittr_1.5
## [4] zlibbioc_1.36.0 lattice_0.20-41 rlang_0.4.8
## [7] stringr_1.4.0 tools_4.0.3 grid_4.0.3
## [10] xfun_0.18 htmltools_0.5.0 yaml_2.2.1
## [13] digest_0.6.27 bookdown_0.21 GenomeInfoDbData_1.2.4
## [16] BiocManager_1.30.10 bitops_1.0-6 RCurl_1.98-1.2
## [19] evaluate_0.14 rmarkdown_2.5 DelayedArray_0.16.0
## [22] stringi_1.5.3 compiler_4.0.3