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

require(singleCellTK)
require(ggplot2)

sce.qc <- params$object

    plotSoupX <- plotSoupXResults(sce.qc, combinePlot = "none")
    i <- "SoupX"
    cat(paste0('# ', i, ' {.tabset} \n\n'))

    cat(paste0('## Scatter Cluster\n\n'))
    plot(plotSoupX$scatter_soupXClusters)
    cat("\n\n")

    for (marker in names(plotSoupX)[-1]) {
        cat(paste0('## Soup Fraction: ', marker, ' \n\n'))
        plot(plotSoupX[[marker]])
        cat("\n\n")
    }

    cat(paste0('## Session info \n\n'))
    soupXMeta <- getSoupX(sce.qc)[[1]]$param
    soupXMeta$sample <- NULL
    soupXMeta$bgBatch <- NULL
    soupXMeta$sessionInfo <- NULL
    soupXMeta
    cat("\n\n")

description_SoupX <- descriptionSoupX()

{.unlisted .unnumbered .toc-ignore}

r description_SoupX

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.