In WeiSong-bio/roryk-bcbioSinglecell: Single-Cell RNA-Seq Utilities

# Last modified 2018-05-08
bcbioSingleCell::prepareSingleCellTemplate()
source("_setup.R")

# Load seurat object
seurat_name <- load(params$seurat_file)
seurat <- get(seurat_name, inherits = FALSE)
stopifnot(is(seurat, "seurat"))
invisible(validObject(seurat))

idents <- levels(seurat@ident)
interesting_groups <- interestingGroups(seurat)

tSNE (all clusters) {.tabset}

groups <- unique(c("ident", "sampleName", interesting_groups))
invisible(lapply(groups, function(group) {
    markdownHeader(group, level = 2, asis = TRUE)
    plotTSNE(seurat, interestingGroups = group) %>%
        show()
}))
rm(groups)

tSNE per cluster {.tabset}

groups <- unique(c("sampleName", interesting_groups))
invisible(lapply(idents, function(ident) {
    subset <- SubsetData(seurat, ident.use = ident)
    markdownHeader(ident, level = 2, asis = TRUE, tabset = TRUE)
    invisible(lapply(groups, function(group) {
        markdownHeader(group, level = 3, asis = TRUE)
        plotTSNE(subset, interestingGroups = group) %>%
            show()
    }))
}))
rm(groups)

Cell counts per cluster {.tabset}

invisible(lapply(idents, function(ident) {
    subset <- SubsetData(seurat, ident.use = ident)
    markdownHeader(ident, level = 2, asis = TRUE, tabset = TRUE)
    master <- subset@meta.data %>%
        uniteInterestingGroups(interestingGroups) %>%
        select(sampleName, interestingGroups)
    sampleStats <- master %>%
        arrange(sampleName) %>%
        group_by(sampleName) %>%
        summarize(count = n()) %>%
        mutate(pct = count / sum(count))
    intgroupStats <- master %>%
        arrange(interestingGroups) %>%
        group_by(interestingGroups) %>%
        summarize(count = n()) %>%
        mutate(pct = count / sum(count))
    kable(sampleStats, digits = 2) %>%
        show()
    kable(intgroupStats, digits = 2) %>%
        show()
}))

Seurat parameters {.tabset}

markdownHeader("PrintPCAParams", level = 2)
PrintPCAParams(seurat)

markdownHeader("PrintFindClustersParams", level = 2)
PrintFindClustersParams(seurat)

markdownHeader("PrintTSNEParams", level = 2)
PrintTSNEParams(seurat)

markdownHeader("PrintSNNParams", level = 2)
PrintSNNParams(seurat)