man/examples/examples_do_BeeSwarmPlot.R

In enblacar/SCpubr: Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

\donttest{
  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_BeeSwarmPlot", passive = TRUE)

  if (isTRUE(value)){
    # Consult the full documentation in https://enblacar.github.io/SCpubr-book/

    # Define your Seurat object.
    sample <- readRDS(system.file("extdata/seurat_dataset_example.rds", package = "SCpubr"))

    # Basic Bee Swarm plot - categorical coloring.
    # This will color based on the unique values of seurat_clusters.
    p <- SCpubr::do_BeeSwarmPlot(sample = sample,
                                 feature_to_rank = "PC_1",
                                 group.by = "seurat_clusters",
                                 continuous_feature = FALSE)

    # Basic Bee Swarm plot - continuous coloring.
    # This will color based on the PC_1 values.
    p <- SCpubr::do_BeeSwarmPlot(sample = sample,
                                 feature_to_rank = "PC_1",
                                 group.by = "seurat_clusters",
                                 continuous_feature = TRUE)
  } else if (base::isFALSE(value)){
    message("This function can not be used without its suggested packages.")
    message("Check out which ones are needed using `SCpubr::state_dependencies()`.")
  }
}