plot_volcano {DEP} | R Documentation

## Volcano plot

### 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)

[Package DEP version 1.2.0 Index]