promor (version 0.2.1)

volcano_plot: Volcano plot

Description

This function generates volcano plots to visualize differentially expressed proteins between groups.

Usage

volcano_plot(
  fit_df,
  adj_method = "BH",
  sig = "adjP",
  cutoff = 0.05,
  lfc = 1,
  line_fc = TRUE,
  line_p = TRUE,
  palette = "viridis",
  text_size = 10,
  label_top = FALSE,
  n_top = 10,
  save = FALSE,
  file_path = NULL,
  file_name = "Volcano_plot",
  file_type = "pdf",
  plot_height = 7,
  plot_width = 7,
  dpi = 80
)

Value

A ggplot2 plot object.

Arguments

fit_df

A fit_df object from performing find_dep.

adj_method

Method used for adjusting the p-values for multiple testing. Default is "BH".

sig

Criteria to denote significance. Choices are "adjP" (default) for adjusted p-value or "P" for p-value.

cutoff

Cutoff value for p-values and adjusted p-values. Default is 0.05.

lfc

Minimum absolute log2-fold change to use as threshold for differential expression.

line_fc

Logical. If TRUE(default), a dotted line will be shown to indicate the lfc threshold in the plot.

line_p

Logical. If TRUE(default), a dotted line will be shown to indicate the p-value or adjusted p-value cutoff.

palette

Viridis color palette option for plots. Default is "viridis". See viridis for available options.

text_size

Text size for axis text, labels etc.

label_top

Logical. If TRUE (default), labels are added to the dots to indicate protein names.

n_top

The number of top hits to label with protein name when label_top = TRUE. Default is 10.

save

Logical. If TRUE saves a copy of the plot in the directory provided in file_path.

file_path

A string containing the directory path to save the file.

file_name

File name to save the plot. Default is "Volcano_plot."

file_type

File type to save the plot. Default is "pdf".

plot_height

Height of the plot. Default is 7.

plot_width

Width of the plot. Default is 7.

dpi

Plot resolution. Default is 80.

Author

Chathurani Ranathunge

Details

• Volcano plots show log-2-fold change on the x-axis, and based on the significance criteria chosen, either -log10(p-value) or -log10(adjusted p-value) on the y-axis.

• volcano_plot requires a fit_df object from performing differential expression analysis with find_dep.

• User has the option to choose criteria that denote significance.

See Also

• find_dep

• topTable and lmFit functions from the limma package.

Examples

## Create a volcano plot with default settings.
volcano_plot(ecoli_fit_df)

## Change significance criteria and cutoff
volcano_plot(ecoli_fit_df, cutoff = 0.1, sig = "P")

## Label top 30 differentially expressed proteins and
## change the color palette of the plot
volcano_plot(ecoli_fit_df, label_top = TRUE, n_top = 30, palette = "mako")