plot_volcano_2var: Generate a volcano plot of genes from a differential...

In BenaroyaResearch/limmaTools: Helper functions for limma analysis and visualization of results

Description

Generate a volcano plot of genes from a differential expression (limma) analysis. This plot can be output to a plotting window, or to a pdf. The points can be colored based on fold-change and p-value thresholds. Points can also be labeled with gene names, and the points to be labeled can be set based on an ellipse oriented to the x- and y-axes.

Usage

plot_volcano_2var(
     topGenes, my_cols=c("darkcyan", "darkorange"),
     file_prefix=NULL, plotdims=c(9,9),
     color_by_threshold=TRUE, fc_cut=log2(1.5), p_cut=0.01,
     x_lim="auto", y_lim="auto",
     gene_labs=NULL, x_cut=0, y_cut=0, x_cut_direction="both",
     gene_labs_repel=TRUE, gene_lab_size=3,
     ...)

Arguments

topGenes	a data frame, typically the output of a call to topTable. Must contain genes, log2 fold-change, and adjusted p-values. Can optionally include a "threshold" column, which should be boolean indicating genes passing significance thresholds.
my_cols	a vector of colors for plotting points. If color_by_threshold is FALSE, only the first element is used. Otherwise, the first and second elements provide the color for points not exceeding and exceeding significance thresholds, respectively.
file_prefix	a character string. If provided, the function outputs a pdf of the plot, named "file_prefix.pdf".
plotdims	a numeric vector, the size (in inches) of the plotting object. Either the size of the pdf, or the size of the plotting window.
color_by_threshold	logical, whether to color points based on exceeding a threshold for logFC and p-value. Used only if fc_cut and p_cut are not NULL.
fc_cut	numeric, the (absolute value) log2 fold-change threshold for determining significance of genes. This value is also plotted as vertical dotted lines. Setting to NULL removes the lines.
p_cut	numeric, the p-value threshold for determining significance of genes. This value is also plotted as a horizontal dotted line. Setting to NULL removes the lines.
x_lim, y_lim	either "auto", NULL, or numeric vectors. If "auto", x- and y-limits are determined from the data using get_xy_lims. If NULL, default plot limits are used. If provided as numeric vectors, the lower and upper limits of the plotting space along the x- and y-axes. Passed to ggplot2::xlim.
gene_labs	character, the type of gene labeling to include. If "threshold". If "ellipse", genes with values outside the labeling ellipse will be labeled. Default value is NULL, which yields no gene labeling.
x_cut, y_cut	numeric. Interpretation depends on the value of gene_labs. If gene_labs == "threshold", these values set the thresholds for logFC and adjusted p-value for labeling the genes; genes will be labeled if -log10 adjusted p-value > y_cut and logFC falls on the side of x_cut specified by x_cut_direction (see below). If gene_labs == "threshold", the x_cut and y_cut specify the radii of the labeling ellipse along the x- and y-axes; genes with values outside the ellipse are labeled with gene names. Both values default to 0, which results in all genes being labeled.
x_cut_direction	character. For threshold-based gene labeling only, specifies the direction of the threshold for gene labeling. Default to "both", which labels genes with absolute value logFC greater than x_cut. "lower" labels genes with logFC less than x_cut; "upper" labels genes with logFC greater than x_cut.
gene_labs_repel	logical, whether to force separation of the gene label text. If TRUE, labels are plotted using geom_text_repel.
gene_lab_size	numeric, the size of the gene label text. Passed to geom_text to geom_text_repel.
...	additional parameters passed to pdf.

BenaroyaResearch/limmaTools documentation built on Dec. 17, 2021, 10:49 a.m.