plot_volcano {DEP} | R Documentation |
plot_volcano
generates a volcano plot for a specified contrast.
plot_volcano(dep, contrast, label_size = 3, add_names = TRUE, adjusted = FALSE, plot = TRUE)
dep |
SummarizedExperiment,
Data object for which differentially enriched proteins are annotated
(output from |
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 |
A volcano plot (generated by ggplot
)
# 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)