Seurat (version 2.3.4)

HTOHeatmap: Hashtag oligo heatmap

Description

Draws a heatmap of hashtag oligo signals across singlets/doublets/negative cells. Allows for the visualization of HTO demultiplexing results.

Usage

HTOHeatmap(object, hto.classification = "hto_classification",
  global.classification = "hto_classification_global", assay.type = "HTO",
  num.cells = 5000, singlet.names = NULL, ...)

Arguments

object

Seurat object. Assumes that the hash tag oligo (HTO) data has been added and normalized, and demultiplexing has been run with HTODemux().

hto.classification

The naming for [e-mail] slot with classification result from HTODemux().

global.classification

The slot for [e-mail] slot specifying a cell as singlet/doublet/negative.

assay.type

Hashtag assay name.

num.cells

Number of cells to plot. Default is to choose 5000 cells by random subsampling, to avoid having to draw exceptionally large heatmaps.

singlet.names

Namings for the singlets. Default is to use the same names as HTOs.

...

Additional arguments for DoHeatmap().

Value

Returns a ggplot2 plot object.

Examples

# NOT RUN {
object <- HTODemux(object)
HTOHeatmap(object)
# }