plot_volcano_de: Make a pretty Volcano plot!

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Make a pretty Volcano plot!

Description

Volcano plots and MA plots provide quick an easy methods to view the set of (in)significantly differentially expressed genes. In the case of a volcano plot, it places the -log10 of the p-value estimate on the y-axis and the fold-change between conditions on the x-axis. Here is a neat snippet from wikipedia: "The concept of volcano plot can be generalized to other applications, where the x-axis is related to a measure of the strength of a statistical signal, and y-axis is related to a measure of the statistical significance of the signal."

Usage

plot_volcano_de(
  table,
  alpha = 0.5,
  color_by = "p",
  color_list = c(`FALSE` = "darkblue", `TRUE` = "darkred"),
  fc_col = "logFC",
  fc_name = "log2 fold change",
  line_color = "black",
  line_position = "bottom",
  logfc = 1,
  p_col = "adj.P.Val",
  p_name = "-log10 p-value",
  p = 0.05,
  shapes_by_state = FALSE,
  minimum_p = NULL,
  size = 2,
  invert = FALSE,
  label = NULL,
  label_column = "hgncsymbol",
  ...
)

Arguments

table	Dataframe from limma's toptable which includes log(fold change) and an adjusted p-value.
alpha	How transparent to make the dots.
color_by	By p-value something else?
color_list	List of colors for significance.
fc_col	Which column contains the fc data?
fc_name	Name of the fold-change to put on the plot.
line_color	What color for the significance lines?
line_position	Put the significance lines above or below the dots?
logfc	Cutoff defining the minimum/maximum fold change for interesting.
p_col	Which column contains the p-value data?
p_name	Name of the p-value to put on the plot.
p	Cutoff defining significant from not.
shapes_by_state	Add fun shapes for the various significance states?
minimum_p	If a pvalue is lower than this, then set it to this, thus artificially limiting the y-scale of a volcano plot. This is only valid if one thinks that the pvalues are artificially low and that is messing with the interpretation of the data.
size	How big are the dots?
invert	Flip the x-axis?
label	Label the top/bottom n logFC values?
label_column	Use this column of annotations for labels instead of rownames?
...	I love parameters!

Value

Ggplot2 volcano scatter plot. This is defined as the -log10(p-value) with respect to log(fold change). The cutoff values are delineated with lines and mark the boundaries between 'significant' and not. This will make a fun clicky googleVis graph if requested.

See Also

[all_pairwise()]

Examples

## Not run: 
 plot_volcano_de(table)
 ## Currently this assumes that a variant of toptable was used which
 ## gives adjusted p-values.  This is not always the case and I should
 ## check for that, but I have not yet.

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.