plot_volcano: Volcano plot of differentially expressed genes

In BIGslu/BIGpicture: Standard Plots for BIGslu

Volcano plot of differentially expressed genes

Description

Volcano plot of differentially expressed genes

Usage

plot_volcano(
  model_result,
  model,
  variables = NULL,
  x = "estimate",
  y = "FDR",
  x_cutoff = NULL,
  y_cutoff = NULL,
  label = NULL,
  genes = NULL,
  genes_label = NULL,
  x.cutoff = NULL,
  y.cutoff = NULL
)

Arguments

model_result	List of data frames output by kimma::kmFit()
model	Character string of model to plot. Must match object names in model_result. For example, "lm", "lme", "lmerel"
variables	Character vector of variables in model_result to include. Default is all variables in model
x	Character string of variable to plot on x-axis. Default is "estimate"
y	Character string of variable to plot on y-axis. Default is "FDR"
x_cutoff	Numeric.Optional x cutoff for color and/or labeling
y_cutoff	Numeric. Optional y cutoff for color and/or labeling
label	Character or numeric. If "all", all significant genes as defined by x_cutoff and y_cutoff are labels with their HGNC symbol. If numeric, that number of most significant genes are labeled.
genes	Data frame with gene metadata for labeling points (optional). If not provided, the gene column in the model_result is used
genes_label	Character string of variable in genes to label with. Required if provide genes parameter
x.cutoff	Deprecated form of x_cutoff
y.cutoff	Deprecated form of y_cutoff

Value

ggplot object

Examples

plot_volcano(example.model, model = "lme")
plot_volcano(example.model, model = "lme", variables = "virus", y = "pval")
plot_volcano(example.model, model = "lme", variables = c("virus","asthma"),
             x_cutoff = 0.5, y_cutoff = 0.05, label = 2)
plot_volcano(example.model, model = "lme", variables = "virus",
             y_cutoff = 0.05, label = 2)
plot_volcano(example.model, model = "lme", variables = "virus",
             x_cutoff = 0.5, label = 2)

plot_volcano(example.model, model = "lme", variables = "virus",
             y_cutoff = 1E-20, label = "all")
plot_volcano(example.model, model = "lme", variables = "virus",
             y_cutoff = 1E-20, label = "all",
             genes = kimma::example.voom$genes, genes_label = "hgnc_symbol")

plot_volcano(example.model, model = "lme", variables = c("virus","asthma"),
             x_cutoff = 0.5, y_cutoff = 1E-1000, label = 2)

BIGslu/BIGpicture documentation built on Oct. 14, 2024, 9:30 p.m.