Last updated: 2019-08-12

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Rmd cbc50e1 Jason Willwerscheid 2019-08-12 wflow_publish(“analysis/droplet.Rmd”) 
droplet <- readRDS("./data/droplet.rds")
source("./code/utils.R")

The droplet-based 3’ scRNA-seq dataset analyzed in Montoro et al. (2018) can be obtained here. It includes counts for 18,388 genes and 7,193 cells. Only 9.3% of all counts are nonzero. The data takes up 143 MB when loaded into memory as a sparse Matrix object.

The original analysis assigns each cell to one of seven cell types. The cells are also labelled according to the mice they come from.

cell.type <- as.factor(sapply(strsplit(colnames(droplet), "_"), `[`, 3))
plot.category(cell.type, title = "Number of Cells per Cell Type")

mouse <- as.factor(sapply(strsplit(colnames(droplet), "_"), `[`, 1))
plot.category(mouse, title = "Number of Cells per Mouse")

Library size is distributed as follows.

plot.libsize(droplet)

Note the presence of extreme outliers. There are two of them, and both turn out to be goblet cells. I think that they should be removed from the dataset before analysis.

table(cell.type[which(colSums(droplet) > 30000)])
#> 
#>          Basal       Ciliated           Club         Goblet       Ionocyte 
#>              0              0              0              2              0 
#> Neuroendocrine           Tuft 
#>              0              0

Mean expression is distributed as follows.

plot.meanexp(droplet)

There are two genes that are on average much more highly expressed than any other gene: Bpifa1 and Scgb1a1. Both have bimodal distributions.

high.exp <- names(which(rowMeans(droplet) > 200))
for (gene in high.exp) {
  plot(plot.gene(droplet, gene))
}


sessionInfo()
#> R version 3.5.3 (2019-03-11)
#> Platform: x86_64-apple-darwin15.6.0 (64-bit)
#> Running under: macOS Mojave 10.14.6
#> 
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] ggplot2_3.2.0 Matrix_1.2-15
#> 
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