plot_volcano: Volcano plot

In arnesmits/DEP: Differential Enrichment analysis of Proteomics data

Description

plot_volcano generates a volcano plot for a specified contrast.

Usage

plot_volcano(dep, contrast, label_size = 3, add_names = TRUE,
  adjusted = FALSE, plot = TRUE)

Arguments

dep	SummarizedExperiment, Data object for which differentially enriched proteins are annotated (output from test_diff() and add_rejections()).
contrast	Character(1), Specifies the contrast to plot.
label_size	Integer(1), Sets the size of name labels.
add_names	Logical(1), Whether or not to plot names.
adjusted	Logical(1), Whether or not to use adjusted p values.
plot	Logical(1), If TRUE (default) the volcano plot is produced. Otherwise (if FALSE), the data which the volcano plot is based on are returned.

Value

A volcano plot (generated by ggplot)

Examples

# Load example
data <- UbiLength
data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",]
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

# Make SummarizedExperiment
columns <- grep("LFQ.", colnames(data_unique))
exp_design <- UbiLength_ExpDesign
se <- make_se(data_unique, columns, exp_design)

# Filter, normalize and impute missing values
filt <- filter_missval(se, thr = 0)
norm <- normalize_vsn(filt)
imputed <- impute(norm, fun = "MinProb", q = 0.01)

# Test for differentially expressed proteins
diff <- test_diff(imputed, "control", "Ctrl")
dep <- add_rejections(diff, alpha = 0.05, lfc = 1)

# Plot volcano
plot_volcano(dep, 'Ubi6_vs_Ctrl', label_size = 5, add_names = TRUE)
plot_volcano(dep, 'Ubi6_vs_Ctrl', label_size = 5,
   add_names = TRUE, adjusted = TRUE)
plot_volcano(dep, 'Ubi6_vs_Ctrl', add_names = FALSE)
plot_volcano(dep, 'Ubi4_vs_Ctrl', label_size = 5, add_names = TRUE)

arnesmits/DEP documentation built on Aug. 7, 2019, 10:44 a.m.