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

require(singleCellTK)
require(celda)
require(knitr)
require(gridExtra)
require(ggplot2)

sce <- params$sce
cluster <- params$cluster
variable <- params$variable
pdf <- params$pdf
showSession <- params$showSession


dev <- ifelse(isTRUE(pdf), c("png"), c("png", "pdf"))
knitr::opts_chunk$set(
  echo = TRUE,
  cache = FALSE,
  cache.lazy = FALSE,
  # don't do lazy-loading for big objects
  cache.comments = FALSE,
  fig.align = "center",
  fig.keep = "all",
  dev = dev
)

Differential Abundance FET

This report will visualize results from the plotClusterAbundance function will visualize the differential abundance in two given variables, by making bar plots that presents the cell counting and fraction in different cases. The analysis presented here shows

plotClusterAbundance(inSCE, cluster, variable, combinePlot = "none")

Session Information

sessionInfo()

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