demux.calls.summary: Plots the number of annotations per sample, per lane

In dtm2451/dittoSeq: User Friendly Single-Cell and Bulk RNA Sequencing Visualization

Plots the number of annotations per sample, per lane

Description

Plots the number of annotations per sample, per lane

Usage

demux.calls.summary(
  object,
  singlets.only = FALSE,
  main = "Sample Annotations by Lane",
  sub = NULL,
  ylab = "Annotations",
  xlab = "Sample",
  color = dittoColors()[2],
  theme = NULL,
  rotate.labels = TRUE,
  data.out = FALSE
)

Arguments

object	A Seurat or SingleCellExperiment object
singlets.only	Whether to only show data for cells called as singlets by demuxlet. Default is TRUE. Note: if doublets are included, only one of their sample calls will be used.
main	plot title. Default = "Sample Annotations by Lane"
sub	plot subtitle
ylab	y axis label, default is "Annotations"
xlab	x axis label, default is "Sample"
color	bars color. Default is the dittoColors skyBlue.
theme	A complete ggplot theme. Default is a slightly modified theme_bw().
rotate.labels	whether sample names / x-axis labels should be rotated or not. Default is TRUE.
data.out	Logical, whether underlying data for the plot should be output instead of the plot itself.

Value

A faceted ggplot summarizing how many cells in each lane were anotated to each sample. Assumes that the Sample calls of each cell, and which lane each cell belonged to, are stored in 'Sample' and 'Lane' metadata slots, respectively, as would be the case if demuxlet information was imported with importDemux.

Alternatively, value will be a data.frame containing the underlying data if data.out = TRUE is provided.

Author(s)

Daniel Bunis

See Also

demux.SNP.summary for plotting the number of SNPs measured per cell. This is the other Demuxlet-associated QC visualization included with dittoSeq.

importDemux, for how to import relevant demuxlet information as metadata.

Kang et al. Nature Biotechnology, 2018 https://www.nature.com/articles/nbt.4042 for more information about the demuxlet cell-sample deconvolution method.

Examples

example(importDemux, echo = FALSE)

demux.calls.summary(myRNA)

# Exclude doublets by setting 'singlets only = TRUE'
demux.calls.summary(myRNA,
    singlets.only = TRUE)

# To return the underlying data.frame
demux.calls.summary(myRNA, data.out = TRUE)

dtm2451/dittoSeq documentation built on April 3, 2024, 9:11 p.m.