Package 'ggvolcano'

Publication-ready volcano plots

Description

Creates a volcano plot to visualize differential expression results. This function is highly configurable to suit publication standards.

Usage

ggvolcano(
  data,
  labels = "",
  logFC_col,
  pval_col,
  x_limits = c(min(data[[logFC_col]], na.rm = TRUE) - 1.5, max(data[[logFC_col]], na.rm =
    TRUE) + 1.5),
  y_limits = NULL,
  xlab = bquote(~Log[2] ~ "fold change"),
  ylab = bquote(~-Log[10] ~ italic(P)),
  title = "Volcano plot",
  subtitle = "",
  caption = paste0("total = ", nrow(data), " variables"),
  pval_cutoff = 1e-06,
  logFC_cutoff = 1,
  cutoff_line = list(type = "longdash", color = "black", width = 0.4),
  point_aes = list(size = 1.5, shape = c(19, 19, 19, 19), color = c("grey30", "#00CD6C",
    "#009ADE", "#FF1F5B"), alpha = 0.9),
  label_aes = list(size = 2.5, color = "black", face = "plain", parse = FALSE),
  legend_aes = list(labels = c("NS", expression(Log[2] ~ FC), "p-value", expression(p -
    value ~ and ~ log[2] ~ FC)), position = "right", label_size = 14, icon_size = 5),
  shade_options = NULL,
  connector_aes = list(line_width = 0.5, arrow_type = "closed", arrow_ends = "first",
    arrow_length = unit(0.01, "npc"), line_color = "grey10", direction = "both",
    draw_arrowheads = TRUE),
  gridlines = list(major = TRUE, minor = TRUE),
  plot_border = "partial",
  border_width = 0.8,
  border_color = "black",
  horizontal_line = NULL,
  horizontal_line_aes = list(type = "longdash", color = "black", width = 0.4)
)

Arguments

data	A data frame containing test statistics. Requires at least columns for variable names, log2 fold changes, and p-values.
labels	Column name, '"rownames"', a single label, or one label per row.
logFC_col	Column name for log2 fold changes.
pval_col	Column name for nominal or adjusted p-values.
x_limits	Limits of the x-axis (default auto-calculated).
y_limits	Limits of the y-axis (default auto-calculated).
xlab	X-axis label.
ylab	Y-axis label.
title	Plot title.
subtitle	Plot subtitle.
caption	Plot caption.
pval_cutoff	P-value cutoff for significance.
logFC_cutoff	Log2 fold-change cutoff for significance.
cutoff_line	List of options for cutoff lines ('type', 'color', 'width').
point_aes	List of aesthetic options for points ('size', 'shape', 'color', 'alpha').
label_aes	List of aesthetic options for labels ('size', 'color', 'face', 'parse').
legend_aes	List of aesthetic options for legend ('labels', 'position', 'label_size', 'icon_size').
shade_options	List of options for shading regions in the plot.
connector_aes	List of aesthetic options for connectors ('line_width', 'arrow_type', 'arrow_ends', 'arrow_length', 'line_color', 'direction', 'draw_arrowheads').
gridlines	List with logical values indicating whether to draw gridlines ('major', 'minor').
plot_border	Add a border for plot axes ('"partial"' or '"full"').
border_width	Width of the border.
border_color	Color of the border.
horizontal_line	Numeric value(s) for drawing horizontal line(s).
horizontal_line_aes	List of aesthetic options for the horizontal line(s) ('type', 'color', 'width').

Value

A ggplot2 object representing the volcano plot.

Examples

data <- read.csv(system.file("extdata", "example.csv", package = "ggvolcano"))

ggvolcano(data,
  logFC_col = "log2FoldChange",
  pval_col = "pvalue",
  pval_cutoff = 10e-4,
  logFC_cutoff = 1.5,
  x_limits = c(-5.5, 5.5),
  y_limits = c(0, -log10(10e-12)),
  title = "Example Volcano plot",
  caption = "FC cutoff, 1.5; p-value cutoff, 10e-4",
  gridlines = list(major = TRUE, minor = TRUE),
  horizontal_line = 10e-8, # Draw horizontal line for p-value cutoff
  horizontal_line_aes = list(type = "dashed", color = "red", width = 0.5)
)

---

Run the Shiny Application

Description

Run the Shiny Application

Usage

run_app(
  onStart = NULL,
  options = list(),
  enableBookmarking = NULL,
  uiPattern = "/",
  ...
)

Arguments

onStart	A function that will be called before the app is actually run. This is only needed for shinyAppObj, since in the shinyAppDir case, a global.R file can be used for this purpose.
options	Named options that should be passed to the runApp call (these can be any of the following: "port", "launch.browser", "host", "quiet", "display.mode" and "test.mode"). You can also specify width and height parameters which provide a hint to the embedding environment about the ideal height/width for the app.
enableBookmarking	Can be one of "url", "server", or "disable". The default value, NULL, will respect the setting from any previous calls to enableBookmarking(). See ?enableBookmarking for more information on bookmarking your app.
uiPattern	A regular expression that will be applied to each GET request to determine whether the ui should be used to handle the request. Note that the entire request path must match the regular expression in order for the match to be considered successful.
...	arguments to pass to golem_opts. See ?golem::get_golem_options for more details.

Value

A Shiny application object.

---