plot_volcano: Create a volcano plot from expression data

In jcalendo/coriell: Convenience Functions for Bioinformatics

Create a volcano plot from expression data

Description

Create a volcano plot from a data.frame containing differential expression results.

Usage

plot_volcano(
  df,
  x = "logFC",
  y = "FDR",
  lab = NULL,
  fdr = 0.05,
  lfc = 0,
  label_sig = FALSE,
  annotate_counts = TRUE,
  up_color = "red2",
  down_color = "royalblue2",
  nonde_color = "grey40",
  up_alpha = 1,
  down_alpha = 1,
  nonde_alpha = 1,
  up_size = 1,
  down_size = 1,
  nonde_size = 1,
  up_shape = 16,
  down_shape = 16,
  nonde_shape = ".",
  xmin_label_offset = 0.8,
  xmax_label_offset = 0.8,
  ymax_label_offset = 0.9,
  lab_size = 6,
  lab_digits = 1,
  x_axis_limits = NULL,
  y_axis_limits = NULL,
  ...
)

Arguments

df	dataframe containing columns with gene names, p-values, and log-fold changes.
x	logFC column. Default (logFC)
y	FDR or p-value column. Default (FDR)
lab	column containing gene id or labels. Default (NULL)
fdr	significance level cutoff for plotting. Values below the given fdr threshold are considered significant. Default (0.05)
lfc	log-fold-change cutoff for plotting. Values greater than the abs(lfc) and less than fdr are displayed as differentially expressed. Default (0)
label_sig	TRUE/FALSE. apply ggrepel::geom_text_labels to significant DE genes.
annotate_counts	TRUE/FALSE. Annotate the plot with the summarized gene counts
up_color	Point color of the up-regulated features
down_color	Point color of the down-regulated features
nonde_color	Point color of the unperturbed features
up_alpha	Point alpha of the up-regulated features
down_alpha	Point alpha of the down-regulated features
nonde_alpha	Point alpha of the unperturbed features
up_size	Point size of the up-regulated features
down_size	Point size of the down-regulated features
nonde_size	Point size of the unperturbed features
up_shape	Point shape of the up-regulated features
down_shape	Point shape of the down-regulated features
nonde_shape	Point shape of the unperturbed features
xmin_label_offset	numeric. Value between 0 and 1 inclusive to control the x-position of the count annotation label for the 'down' counts
xmax_label_offset	numeric. Value between 0 and 1 inclusive to control the x-position of the count annotation label for the 'up' counts
ymax_label_offset	numeric. Value between 0 and 1 inclusive to control the y-position of the count labels.
lab_size	numeric. Size of the label if annotate_counts = TRUE. Default 6.
lab_digits	numeric. The number of digits used when rounding percentage values when annotate_counts=TRUE. Default (1)
x_axis_limits	numeric vector of axis limits supplied to ggplot2::coord_cartesian(). Default (NULL)
y_axis_limits	numeric vector of axis limits supplied to ggplot2::coord_cartesian(). Default (NULL)
...	Additional arguments passed to ggrepel::geom_text_repel

Value

ggplot volcano plot

Examples

plot_volcano(GSE161650_de, fdr = 0.01, lfc = log2(2))

jcalendo/coriell documentation built on March 5, 2025, 5:42 a.m.