plot_volcano {ideal} | R Documentation

## Volcano plot for log fold changes and log p-values

### Description

Volcano plot for log fold changes and log p-values in the ggplot2 framework, with additional support to annotate genes if provided.

### Usage

    plot_volcano(res_obj, FDR = 0.05, ylim_up = NULL, vlines = NULL,
      title = NULL, intgenes = NULL, intgenes_color = "steelblue",
      labels_intgenes = TRUE)

### Arguments

`res_obj` | A `DESeqResults` object
`FDR` | Numeric value, the significance level for thresholding adjusted p-values
`ylim_up` | Numeric value, Y axis upper limits to restrict the view
`vlines` | The x coordinate (in absolute value) where to draw vertical lines, optional
`title` | A title for the plot, optional
`intgenes` | Vector of genes of interest. Gene symbols if a `symbol` column is provided in `res_obj`, or else the identifiers specified in the row names
`intgenes_color` | The color to use to mark the genes on the main plot.
`labels_intgenes` | Logical, whether to add the gene identifiers/names close to the marked plots

### Details

The genes of interest are to be provided as gene symbols if a `symbol` column is provided in `res_obj`, or else b< using the identifiers specified in the row names

### Value

An object created by `ggplot`

### Examples

    library(airway)
    data(airway)
    airway
    dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                                 colData = colData(airway),
                                                 design=~cell+dex)

    # subsetting for quicker run, ignore the next two commands if regularly using the function
    gene_subset <- c(
      "ENSG00000103196",  # CRISPLD2
      "ENSG00000120129",  # DUSP1
      "ENSG00000163884",  # KLF15
      "ENSG00000179094",  # PER1
      rownames(dds_airway)[rep(c(rep(FALSE,99), TRUE), length.out=nrow(dds_airway))]) # 1% of ids
    dds_airway <- dds_airway[gene_subset,]

    dds_airway <- DESeq2::DESeq(dds_airway)
    res_airway <- DESeq2::results(dds_airway)

    plot_volcano(res_airway)

[Package ideal version 1.8.1 Index]