do_VolcanoPlot: Compute a Volcano plot out of DE genes.

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

Compute a Volcano plot out of DE genes.

Description

Compute a Volcano plot out of DE genes.

Usage

do_VolcanoPlot(
  sample,
  de_genes,
  pval_cutoff = 0.05,
  FC_cutoff = 2,
  pt.size = 2,
  border.size = 1.5,
  border.color = "black",
  font.size = 14,
  font.type = "sans",
  plot.title = NULL,
  plot.subtitle = NULL,
  plot.caption = NULL,
  plot_lines = TRUE,
  line_color = "grey75",
  line_size = 0.5,
  add_gene_tags = TRUE,
  add_tag_side = "both",
  order_tags_by = "both",
  tag_size = 6,
  n_genes = 5,
  use_labels = FALSE,
  colors.use = "steelblue",
  plot.title.face = "bold",
  plot.subtitle.face = "plain",
  plot.caption.face = "italic",
  axis.title.face = "bold",
  axis.text.face = "plain",
  legend.title.face = "bold",
  legend.text.face = "plain"
)

Arguments

sample	Seurat | A Seurat object, generated by CreateSeuratObject.
de_genes	tibble | Output of Seurat::FindMarkers().
pval_cutoff	numeric | Cutoff for the p-value.
FC_cutoff	numeric | Cutoff for the avg_log2FC.
pt.size	numeric | Size of the dots.
border.size	numeric | Width of the border of the cells.
border.color	character | Color for the border of the heatmap body.
font.size	numeric | Overall font size of the plot. All plot elements will have a size relationship with this font size.
font.type	character | Base font family for the plot. One of: mono: Mono spaced font. serif: Serif font family. sans: Default font family.
plot.title, plot.subtitle, plot.caption	character | Title, subtitle or caption to use in the plot.
plot_lines	logical | Whether to plot the division lines.
line_color	character | Color for the lines.
line_size	numeric | Size of the lines in the plot.
add_gene_tags	logical | Whether to plot the top genes.
add_tag_side	logical | Either "both", "positive" or "negative" to indicate which side of genes to tag
order_tags_by	character | Either "both", "pvalue" or "logfc".
tag_size	numeric | Size of the text/label for the tags.
n_genes	numeric | Number of top genes to plot.
use_labels	logical | Whether to use labels instead of text for the tags.
colors.use	character | Color to generate a tetradic color scale with.
plot.title.face, plot.subtitle.face, plot.caption.face, axis.title.face, axis.text.face, legend.title.face, legend.text.face	character | Controls the style of the font for the corresponding theme element. One of: plain: For normal text. italic: For text in itallic. bold: For text in bold. bold.italic: For text both in itallic and bold.

Value

A volcano plot as a ggplot2 object.

Examples

  # Check Suggests.
  value <- SCpubr:::check_suggests(function_name = "do_VolcanoPlot", 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"))

    # Retrieve DE genes.
    de_genes <- readRDS(system.file("extdata/de_genes_example.rds", package = "SCpubr"))

    # Generate a volcano plot.
    p <- SCpubr::do_VolcanoPlot(sample = sample,
                                de_genes = de_genes)
    p

  } 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()`.")
  }

enblacar/SCpubr documentation built on Aug. 25, 2024, 9:45 p.m.