- Loading Packages and Data
- Logarithmic Transformation of Counts
- KODAMA Analysis and Visualization with UMAP
- Visualizing Spatial Coordinates
SpatialExperiment
Last updated: 2024-07-19
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Knit directory: KODAMA-Analysis/
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Spatial Transcriptomics has revolutionized the study of tissue architecture by integrating spatial information with transcriptomic data. This tutorial demonstrates how to perform spatial data analysis and visualize the results. We will use a dataset from the mouse olfactory bulb (OB), acquired via the Spatial Transcriptomics platform (Stahl et al. 2016) link to the article. This dataset includes annotations for five cellular layers as provided by the original authors.
Spatial Transcriptomics enables researchers to explore the spatial organization of gene expression within tissues, offering insights into cellular interactions and tissue microenvironments. By combining spatial coordinates with gene expression profiles, analyses such as Principal Component Analysis (PCA) and visualization techniques like KODAMA provide powerful tools to uncover spatial patterns and relationships in biological data. # Tutorial Steps
Loading Packages and Data
library(SpatialExperiment)
library(STexampleData)
library(scran)
library(scater)
library(KODAMA)
library(KODAMAextra)
# Loading spatial data from the mouse olfactory bulb
spe = ST_mouseOB()Extracting and Handling Cell Metadata
# Extracting cell metadata
metaData = SingleCellExperiment::colData(spe)
# Calculating library factors
spe <- computeLibraryFactors(spe)
# Summarizing size factors
summary(sizeFactors(spe)) Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0001259 0.6490732 0.9197538 1.0000000 1.3239172 2.3464869 Logarithmic Transformation of Counts
spe <- logNormCounts(spe)Principal Component Analysis (PCA)
# Selecting highly variable genes
top_hvgs <- getTopHVGs(spe, prop = 0.1)
# Performing PCA
spe <- runPCA(spe, 50, subset_row = top_hvgs, scale = TRUE)
# Defining colors for PCA plot based on "layer" metadata
colors = c("#11111199", "#111ee199", "#aa111199", "#1111cc99", "#11cccc99")
plot(reducedDim(spe, type = "PCA"), bg = colors[as.factor(metaData[,"layer"])], pch = 21, cex = 2)
KODAMA Analysis and Visualization with UMAP
# Running KODAMA on the reduced PCA matrix
spe = RunKODAMAmatrix(spe, reduction = "PCA")socket cluster with 1 nodes on host 'localhost'
================================================================================[1] "Finished parallel computation"
[1] "Calculation of dissimilarity matrix..."
================================================================================# Visualizing KODAMA using UMAP method
spe = RunKODAMAvisualization(spe, method = "UMAP")Visualizing Spatial Coordinates
# Retrieving spatial coordinates
xy = spatialCoords(spe)
# Plotting reduced data with KODAMA, based on "layer" metadata
plot(reducedDim(spe, type = "KODAMA"), bg = colors[as.factor(metaData[,"layer"])], pch = 21, cex = 2)
# Plotting spatial coordinates, based on "layer" metadata
plot(xy, bg = colors[as.factor(metaData[,"layer"])], pch = 21, cex = 2)
sessionInfo()R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[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
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] KODAMAextra_1.0 e1071_1.7-14
[3] doParallel_1.0.17 iterators_1.0.14
[5] foreach_1.5.2 KODAMA_3.1
[7] umap_0.2.10.0 Rtsne_0.17
[9] minerva_1.5.10 scater_1.32.0
[11] ggplot2_3.5.1 scran_1.32.0
[13] scuttle_1.14.0 STexampleData_1.12.3
[15] ExperimentHub_2.12.0 AnnotationHub_3.12.0
[17] BiocFileCache_2.12.0 dbplyr_2.5.0
[19] SpatialExperiment_1.14.0 SingleCellExperiment_1.26.0
[21] SummarizedExperiment_1.34.0 Biobase_2.64.0
[23] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1
[25] IRanges_2.38.1 S4Vectors_0.42.1
[27] BiocGenerics_0.50.0 MatrixGenerics_1.16.0
[29] matrixStats_1.3.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] rstudioapi_0.16.0 jsonlite_1.8.8
[3] magrittr_2.0.3 ggbeeswarm_0.7.2
[5] magick_2.8.4 rmarkdown_2.27
[7] fs_1.6.4 zlibbioc_1.50.0
[9] vctrs_0.6.5 memoise_2.0.1
[11] DelayedMatrixStats_1.26.0 askpass_1.2.0
[13] htmltools_0.5.8.1 S4Arrays_1.4.1
[15] curl_5.2.1 BiocNeighbors_1.22.0
[17] SparseArray_1.4.8 sass_0.4.9
[19] bslib_0.7.0 cachem_1.1.0
[21] whisker_0.4.1 igraph_2.0.3
[23] mime_0.12 lifecycle_1.0.4
[25] pkgconfig_2.0.3 rsvd_1.0.5
[27] Matrix_1.7-0 R6_2.5.1
[29] fastmap_1.2.0 GenomeInfoDbData_1.2.12
[31] digest_0.6.36 colorspace_2.1-0
[33] AnnotationDbi_1.66.0 ps_1.7.7
[35] rprojroot_2.0.4 RSpectra_0.16-1
[37] dqrng_0.4.1 irlba_2.3.5.1
[39] RSQLite_2.3.7 beachmat_2.20.0
[41] filelock_1.0.3 fansi_1.0.6
[43] httr_1.4.7 abind_1.4-5
[45] compiler_4.4.1 proxy_0.4-27
[47] bit64_4.0.5 withr_3.0.0
[49] BiocParallel_1.38.0 viridis_0.6.5
[51] DBI_1.2.3 highr_0.11
[53] openssl_2.2.0 rappdirs_0.3.3
[55] DelayedArray_0.30.1 rjson_0.2.21
[57] bluster_1.14.0 tools_4.4.1
[59] vipor_0.4.7 beeswarm_0.4.0
[61] httpuv_1.6.15 glue_1.7.0
[63] callr_3.7.6 promises_1.3.0
[65] grid_4.4.1 getPass_0.2-4
[67] cluster_2.1.6 snow_0.4-4
[69] generics_0.1.3 gtable_0.3.5
[71] class_7.3-22 BiocSingular_1.20.0
[73] ScaledMatrix_1.12.0 metapod_1.12.0
[75] utf8_1.2.4 XVector_0.44.0
[77] ggrepel_0.9.5 BiocVersion_3.19.1
[79] pillar_1.9.0 stringr_1.5.1
[81] limma_3.60.3 later_1.3.2
[83] dplyr_1.1.4 lattice_0.22-6
[85] bit_4.0.5 tidyselect_1.2.1
[87] locfit_1.5-9.10 Biostrings_2.72.1
[89] knitr_1.48 git2r_0.33.0
[91] gridExtra_2.3 edgeR_4.2.1
[93] xfun_0.45 statmod_1.5.0
[95] stringi_1.8.4 UCSC.utils_1.0.0
[97] yaml_2.3.9 evaluate_0.24.0
[99] codetools_0.2-20 tibble_3.2.1
[101] BiocManager_1.30.23 cli_3.6.3
[103] reticulate_1.38.0 munsell_0.5.1
[105] processx_3.8.4 jquerylib_0.1.4
[107] Rcpp_1.0.12 doSNOW_1.0.20
[109] png_0.1-8 blob_1.2.4
[111] sparseMatrixStats_1.16.0 viridisLite_0.4.2
[113] scales_1.3.0 purrr_1.0.2
[115] crayon_1.5.3 rlang_1.1.4
[117] KEGGREST_1.44.1