demux.SNP.summary: Plots the number of SNPs sequenced per droplet

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

Plots the number of SNPs sequenced per droplet

Description

Plots the number of SNPs sequenced per droplet

Usage

demux.SNP.summary(
  object,
  group.by = "Lane",
  color.by = group.by,
  plots = c("jitter", "boxplot"),
  boxplot.color = "grey30",
  add.line = 50,
  min = 0,
  ...
)

Arguments

object	A Seurat or SingleCellExperiment object
group.by	String "name" of a metadata to use for grouping values. Default is "Lane".
color.by	String "name" of a metadata to use for coloring. Default is whatever was provided to group.by.
plots	String vector which sets the types of plots to include: possibilities = "jitter", "boxplot", "vlnplot", "ridgeplot". NOTE: The order matters, so use c("back","middle","front") when inputing multiple to put them in the order you want.
boxplot.color	The color of the lines of the boxplot.
add.line	numeric value(s) where a dashed horizontal line should go. Default = 50, a high confidence minimum number of SNPs per cell for highly accurate demuxlet sample deconvolution.
min	numeric value which sets the minimum value shown on the y-axis.
...	extra arguments passed to dittoPlot

Details

This function is a wrapper that essentially runs dittoPlot("demux.N.SNP") with a few modified defaults. The altered defaults:

• Data is grouped and colored by the "Lane" metadata (unless group.by or color.by are adjusted otherwise).

• Data is displayed as boxplots with gray lines on top of dots for individual cells (unless plots or boxplot.color are adjusted otherwise).

• The plot is set to have minimum y axis value of zero (unless min is adjusted otherwise).

• A dashed line is added at the value 50, a very conservative minimum number of SNPs for high confidence sample calls (unless add.line is adjusted otherwise).

Value

A ggplot, made with dittoPlot showing a summary of how many SNPs were available to Demuxlet for each cell of a dataset.

Alternatively, a plotly object if data.hover = TRUE is provided.

Alternatively, list containing a ggplot and the underlying data as a dataframe if data.out = TRUE is provided.

Author(s)

Daniel Bunis

See Also

demux.calls.summary for plotting the number of sample annotations assigned within each lane. This is the other Demuxlet-associated QC visualization included with dittoSeq.

dittoPlot, as demux.SNP.summary is essentially just a dittoPlot wrapper.

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.SNP.summary(myRNA)

#Function wraps dittoPlot. See dittoPlot docs for more examples

dtm2451/DittoSeq documentation built on May 4, 2024, 7:31 a.m.