Seurat (version 3.1.1)

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, assay = "HTO", classification = paste0(assay,
  "_classification"), global.classification = paste0(assay,
  "_classification.global"), ncells = 5000, singlet.names = NULL,
  raster = TRUE)

Arguments

object

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

assay

Hashtag assay name.

classification

The naming for metadata column with classification result from HTODemux().

global.classification

The slot for metadata column specifying a cell as singlet/doublet/negative.

ncells

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.

raster

If true, plot with geom_raster, else use geom_tile. geom_raster may look blurry on some viewing applications such as Preview due to how the raster is interpolated. Set this to FALSE if you are encountering that issue (note that plots may take longer to produce/render).

Value

Returns a ggplot2 plot object.

See Also

HTODemux

Examples

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