Comprehensive reporting of QC metrics: contamination identification using decontX"

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

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

sce.qc<- params$object

    plotDecontX<- suppressWarnings(plotDecontXResults(sce.qc, reducedDimName = "UMAP"))
    i="DecontX"
    cat(paste0('# ', i, ' {.tabset} \n\n'))
    cat(paste0('## Scatter Score \n\n'))
    plotDecontX$scatter_decontXContamination

    cat(paste0('## Scatter Clusters \n\n'))
    plotDecontX$scatter_decontXClusters

    cat(paste0('## Density Score \n\n'))
    plotDecontX$density_decontXContamination

    cat(paste0('## Violin Score \n\n'))
    plotDecontX$violin_decontXContamination

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

description_DecontX<- descriptionDecontX()

{.unlisted .unnumbered .toc-ignore}

r description_DecontX

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