draw_volcano: Volcano Plot

In egenn/rtemis: Machine Learning and Visualization

Volcano Plot

Description

Volcano Plot

Usage

draw_volcano(
  x,
  pvals,
  xnames = NULL,
  group = NULL,
  x_thresh = 0,
  p_thresh = 0.05,
  p_transform = function(x) -log10(x),
  p_adjust_method = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr",
    "none"),
  legend = NULL,
  legend_lo = NULL,
  legend_hi = NULL,
  label_lo = "Low",
  label_hi = "High",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  margin = list(b = 65, l = 65, t = 50, r = 10, pad = 0),
  xlim = NULL,
  ylim = NULL,
  alpha = NULL,
  hline = NULL,
  hline_col = NULL,
  hline_width = 1,
  hline_dash = "solid",
  hline_annotate = NULL,
  hline_annotation_x = 1,
  annotate = TRUE,
  annotate_col = theme[["labs_col"]],
  theme = choose_theme(),
  font_size = 16,
  palette = NULL,
  legend_x_lo = NULL,
  legend_x_hi = NULL,
  legend_y = 0.97,
  annotate_n = 7,
  ax_lo = NULL,
  ay_lo = NULL,
  ax_hi = NULL,
  ay_hi = NULL,
  annotate_alpha = 0.7,
  hovertext = NULL,
  displayModeBar = FALSE,
  filename = NULL,
  file_width = 500,
  file_height = 500,
  file_scale = 1,
  verbosity = 1L,
  ...
)

Arguments

x	Numeric vector: Input values, e.g. log2 fold change, coefficients, etc.
pvals	Numeric vector: p-values.
xnames	Character vector: x names.
group	Factor: Used to color code points. If NULL, significant points below x_thresh, non-significant points, and significant points above x_thresh will be plotted with the first, second and third color of palette.
x_thresh	Numeric x-axis threshold separating low from high.
p_thresh	Numeric: p-value threshold of significance.
p_transform	function.
p_adjust_method	Character: p-value adjustment method. "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". Default = "holm". Use "none" for raw p-values.
legend	Logical: If TRUE, show legend. Will default to FALSE, if group = NULL, otherwise to TRUE.
legend_lo	Character: Legend to annotate significant points below the x_thresh.
legend_hi	Character: Legend to annotate significant points above the x_thresh.
label_lo	Character: label for low values.
label_hi	Character: label for high values.
main	Character: Main title.
xlab	Character: x-axis label.
ylab	Character: y-axis label.
margin	Named list of plot margins. Default = list(b = 65, l = 65, t = 50, r = 10, pad = 0).
xlim	Numeric vector, length 2: x-axis limits.
ylim	Numeric vector, length 2: y-axis limits.
alpha	Numeric: point transparency.
hline	Numeric: If defined, draw a horizontal line at this y value.
hline_col	Color for hline.
hline_width	Numeric: Width for hline.
hline_dash	Character: Type of line to draw: "solid", "dot", "dash", "longdash", "dashdot", or "longdashdot".
hline_annotate	Character: Text of horizontal line annotation if hline is set.
hline_annotation_x	Numeric: x position to place annotation with paper as reference. 0: to the left of the plot area; 1: to the right of the plot area.
annotate	Logical: If TRUE, annotate significant points.
annotate_col	Color for annotations.
theme	Theme object.
font_size	Integer: Font size.
palette	Character: Name of rtemis palette to use.
legend_x_lo	Numeric: x position of legend_lo.
legend_x_hi	Numeric: x position of legend_hi.
legend_y	Numeric: y position for legend_lo and legend_hi.
annotate_n	Integer: Number of significant points to annotate.
ax_lo	Numeric: Sets the x component of the arrow tail about the arrow head for significant points below x_thresh.
ay_lo	Numeric: Sets the y component of the arrow tail about the arrow head for significant points below x_thresh.
ax_hi	Numeric: Sets the x component of the arrow tail about the arrow head for significant points above x_thresh.
ay_hi	Numeric: Sets the y component of the arrow tail about the arrow head for significant points above x_thresh.
annotate_alpha	Numeric: Transparency for annotations.
hovertext	Character vector: Text to display on hover.
displayModeBar	Logical: If TRUE, display plotly mode bar.
filename	Character: Path to save the plot image.
file_width	Numeric: Width of the saved plot image.
file_height	Numeric: Height of the saved plot image.
file_scale	Numeric: Scale of the saved plot image.
verbosity	Integer: Verbosity level.
...	Additional parameters passed to draw_scatter.

Value

plotly object.

Author(s)

EDG

Examples

## Not run: 
set.seed(2019)
x <- rnormmat(500, 500)
y <- x[, 3] + x[, 5] - x[, 9] + x[, 15] + rnorm(500)
mod <- massGLM(y, x)
draw_volcano(mod$summary$`Coefficient y`, mod$summary$`p_value y`)

## End(Not run)

egenn/rtemis documentation built on June 14, 2025, 11:54 p.m.