Comprehensive reporting of QC metrics: identifying doublets with Scrublet"

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

require(singleCellTK)
require(umap)
require(ggplot2)

sce.qc<- params$object

    plotsScrublet<- suppressWarnings(plotScrubletResults(sce.qc, reducedDimName="UMAP"))
    i="Scrublet"
    cat(paste0('# ', i, ' {.tabset .tabset-fade} \n\n'))
    cat(paste0('## Scatter Score \n\n'))
    plotsScrublet$scatter_doubletScore

    cat(paste0('## Scatter Call \n\n'))
    plotsScrublet$scatter_doubletCall

    cat(paste0('## Density Score \n\n'))
    plotsScrublet$density_doubletScore

    cat(paste0('## Violin Score \n\n'))
    plotsScrublet$violin_doubletScore

    cat(paste0('## Session info \n\n'))
    sce.qc@metadata$runScrublet

description_Scrublet <- descriptionScrublet()

{.unlisted .unnumbered .toc-ignore}

r description_Scrublet

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.