Basic quality control on scRNA-seq data with ClickTag barcodes
Kayla Jackson and A. Sina Booeshaghi
2023-11-30
Source:vignettes/vig11_clicktags.Rmd
vig11_clicktags.RmdIntroduction
The data in this vignette is shipped with the cellatlas
repository. The count matrix and metadata are provided in the
cellatlas/examples folder as an AnnData
object. We will begin by loading the object and converting it to a
SingleCellExperiment object.
library(stringr)
library(DropletUtils)
library(Matrix)
library(SpatialExperiment)
library(SpatialFeatureExperiment)
library(scater)
library(scuttle)
library(Voyager)
library(ggplot2)
theme_set(theme_bw())
if (!file.exists("clicktags.rds"))
download.file("https://github.com/pachterlab/voyager/raw/documentation-devel/vignettes/clicktags.rds", destfile = "clicktags.rds")
sce <- readRDS("clicktags.rds")
sce <- addPerCellQCMetrics(sce)
names(colData(sce))
#> [1] "sum" "detected" "total"
plotColData(sce, "sum") +
plotColData(sce, "detected") 
plotColData(sce, x = "sum", y = "detected", bins = 100) +
scale_fill_distiller(palette = "Blues", direction = 1)
#> Scale for fill is already present.
#> Adding another scale for fill, which will replace the existing scale.
bcrank <- barcodeRanks(counts(sce))
knee <- metadata(bcrank)$knee
inflection <- metadata(bcrank)$inflection
plot(bcrank$rank, bcrank$total, log="xy",
xlab="Rank", ylab="Total ClickTags count", cex.lab=1.2)
#> Warning in xy.coords(x, y, xlabel, ylabel, log): 1 y value <= 0 omitted from
#> logarithmic plot
abline(h=inflection, col="darkgreen", lty=2)
abline(h=knee, col="dodgerblue", lty=2)
sce <- sce[, colSums(counts(sce)) > inflection]
sce
#> class: SingleCellExperiment
#> dim: 20 3368
#> metadata(0):
#> assays(1): counts
#> rownames(20): ClickTag1 ClickTag2 ... ClickTag19 ClickTag20
#> rowData names(1): feature_name
#> colnames(3368): AAACCTGCAAACTGCT AAACCTGGTAGCTTGT ... TTTGTCAGTCACCCAG
#> TTTGTCATCTCTTATG
#> colData names(3): sum detected total
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
sessionInfo()
#> R version 4.3.2 (2023-10-31)
#> Platform: x86_64-apple-darwin20 (64-bit)
#> Running under: macOS Ventura 13.6
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
#>
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#>
#> time zone: UTC
#> tzcode source: internal
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] Voyager_1.4.0 scater_1.30.0
#> [3] ggplot2_3.4.4 scuttle_1.12.0
#> [5] SpatialFeatureExperiment_1.3.0 SpatialExperiment_1.12.0
#> [7] Matrix_1.6-3 DropletUtils_1.22.0
#> [9] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
#> [11] Biobase_2.62.0 GenomicRanges_1.54.1
#> [13] GenomeInfoDb_1.38.1 IRanges_2.36.0
#> [15] S4Vectors_0.40.2 BiocGenerics_0.48.1
#> [17] MatrixGenerics_1.14.0 matrixStats_1.1.0
#> [19] stringr_1.5.1
#>
#> loaded via a namespace (and not attached):
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#> [3] wk_0.9.0 magrittr_2.0.3
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#> [17] terra_1.7-55 htmltools_0.5.7
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#> [33] pkgconfig_2.0.3 rsvd_1.0.5
#> [35] R6_2.5.1 fastmap_1.1.1
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