man/examples/examples_do_DotPlot.R

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

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

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

    # Basic Dot plot.
    p <- SCpubr::do_DotPlot(sample = sample,
                            features = "EPC1")

    # Querying multiple features.
    genes <- rownames(sample)[1:14]
    p <- SCpubr::do_DotPlot(sample = sample,
                            features = genes)

    # Inverting the axes.
    p <- SCpubr::do_DotPlot(sample = sample,
                            features = genes,
                            cluster = TRUE,
                            plot.title = "Clustered",
                            flip = TRUE)

    # Modifying default colors.
    # Two colors to generate a gradient.
    p <- SCpubr::do_DotPlot(sample = sample,
                            features = genes,
                            colors.use = c("#001219", "#e9d8a6"))

    # Querying multiple features as a named list - splitting by each item in list.
    # Genes have to be unique.
    genes <- list("Naive CD4+ T" = rownames(sample)[1:2],
                  "EPC1+ Mono" = rownames(sample)[3:4],
                  "Memory CD4+" = rownames(sample)[5],
                  "B" = rownames(sample)[6],
                  "CD8+ T" = rownames(sample)[7],
                  "FCGR3A+ Mono" = rownames(sample)[8:9],
                  "NK" = rownames(sample)[10:11],
                  "DC" = rownames(sample)[12:13],
                  "Platelet" = rownames(sample)[14])

    p <- SCpubr::do_DotPlot(sample = sample,
                            features = genes)

    # Clustering the identities.
    p <- SCpubr::do_DotPlot(sample = sample,
                            features = genes,
                            cluster = TRUE,
                            plot.title = "Clustered")
  } 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()`.")
  }
}