plot_UCell_scores {scGate}

Plot UCell scores by level

Description

Show distribution of UCell scores for each level of a given scGate model

Usage

plot_UCell_scores(
  obj,
  model,
  overlay = 5,
  pos.thr = 0.2,
  neg.thr = 0.2,
  ncol = NULL,
  combine = TRUE
)

Arguments

obj

Gated Seurat object (output of scGate)

model

scGate model used to identify a target population in obj

overlay

Degree of overlay for ggridges

pos.thr

Threshold for positive signatures used in scGate model (set to NULL to disable)

neg.thr

Threshold for negative signatures used in scGate model (set to NULL to disable)

ncol

Number of columns in output object (passed to wrap_plots)

combine

Whether to combine plots into a single object, or to return a list of plots

Value

Returns a density plot of UCell scores for the signatures in the scGate model, for each level of the model

Either a plot combined by patchwork (combine=T) or a list of plots (combine=F)

Examples

scGate.model.db <- get_scGateDB()
model <- scGate.model.db$human$generic$Tcell
# Apply scGate with this model
data(query.seurat)
query.seurat <- scGate(query.seurat, model=model,
    reduction="pca", save.levels=TRUE)
# View UCell score distribution
plot_UCell_scores(query.seurat, model)