module plot

create combined violin and boxplot of the module score

Usage

ModulePlot(x_var, module, object, color)

Arguments

x_var

variable in meta data which represents the x-axis

module

variable in meta data of the module score

object

Seurat object

color

color palette

Value

plot module plot

Examples

library(Seurat)
#> Loading required package: SeuratObject
#> Loading required package: sp
#> ‘SeuratObject’ was built under R 4.4.0 but the current version is
#> 4.4.2; it is recomended that you reinstall ‘SeuratObject’ as the ABI
#> for R may have changed
#> 
#> Attaching package: ‘SeuratObject’
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, t
set.seed(123)
pbmc_small$AIE_type <- sample(c("control", "CASPR2", "LGI1"), ncol(pbmc_small), replace = TRUE)
module1 <- list(c(rownames(pbmc_small)[1:100]))
pbmc_small <- AddModuleScore(
  pbmc_small,
  features = module1,
  assay = "RNA",
  name = "module",
  ctrl = 5
)
ModulePlot(
  x_var = "AIE_type",
  module = "module1",
  object = pbmc_small,
  color = c("control" = "blue", "CASPR2" = "red", "LGI1" = "green")
)
#> Warning: Using formula(x) is deprecated when x is a character vector of length > 1.
#>   Consider formula(paste(x, collapse = " ")) instead.