Plot scGate filtering results by level — plot

Fast plotting of gating results over each model level.

Usage

plot_levels(obj, pure.col = "green", impure.col = "gray")

Arguments

obj: Gated Seurat object output of scGate filtering function
pure.col: Color code for pure category
impure.col: Color code for impure category

Value

UMAP plots with 'Pure'/'Impure' labels for each level of the scGate model

Examples

# \donttest{
scGate.model.db <- get_scGateDB()
#> Using local version of repo scGate_models-master. If you want update it, set option force_update = TRUE
model <- scGate.model.db$human$generic$Myeloid
# Apply scGate with this model
data(query.seurat)
query.seurat <- scGate(query.seurat, model=model,
    reduction="pca", save.levels=TRUE)
#> 
#> ### Detected a total of 79 pure 'Target' cells (26.33% of total)
library(patchwork)     
#> Warning: package 'patchwork' was built under R version 4.4.1
pll <- plot_levels(query.seurat)
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> i Please use tidy evaluation idioms with `aes()`.
#> i See also `vignette("ggplot2-in-packages")` for more information.
#> i The deprecated feature was likely used in the Seurat package.
#>   Please report the issue at <https://github.com/satijalab/seurat/issues>.
wrap_plots(pll)

# }