vsVolcanoMatrix {vidger} | R Documentation

## Volcano plot matrix from log_{2} fold changes and -log_{10}(p-values)

### Description

This function allows you to extract necessary results-based data from either a `DESeq2` object, `edgeR` object, or `cuffdiff` data frame to create a volcano plot (i.e. a scatter plot) of the negative log of the p-value versus the log of the fold change while implementing ggplot2 aesthetics for all possible combinations of treatments.

### Usage

    vsVolcanoMatrix(data, d.factor = NULL, type = c("cuffdiff", "deseq",
      "edger"), padj = 0.05, x.lim = NULL, lfc = NULL, title = TRUE,
      legend = TRUE, grid = TRUE, counts = TRUE, data.return = FALSE,
      xaxis.text.size = 9, yaxis.text.size = 9, xaxis.title.size = 10,
      yaxis.title.size = 10, main.title.size = 15, legend.text.size = 9,
      facet.title.size = 10)

### Arguments

`data` | a cuffdiff, DESeq2, or edgeR object.
`d.factor` | a specified factor; for use with DESeq2 objects only. Defaults to `NULL`
`type` | an analysis classifier to tell the function how to process the data. Must be either `cuffdiff`, `deseq`, or `edgeR`.
`padj` | a user defined adjusted p-value cutoff point. Defaults to `0.05`.
`x.lim` | set manual limits to the x axis. Defaults to `NULL`.
`lfc` | log fold change level for setting conditonals. If no user input is added (`NULL`), value defaults to `1`.
`title` | show title of plot. Defaults to `TRUE`.
`legend` | shows legend of plot. Defaults to `TRUE`.
`grid` | show major and minor axis lines. Defaults to `TRUE`.
`counts` | displays the number of differentially expressed genes for each treatment comparison. Defaults to `TRUE`.
`data.return` | returns data output of plot if set to `TRUE`. Defaults to `FALSE`.
`xaxis.text.size` | change the font size of the `x`-axis text. Defaults to `9`.
`yaxis.text.size` | change the font size of the `y`-axis text. Defaults to `9`.
`xaxis.title.size` | change the font size of the `x`-axis title text. Defaults to `10`.
`yaxis.title.size` | change the font size of the `y`-axis title text. Defaults to `10`.
`main.title.size` | change the font size of the plot title text. Defaults to `15`.
`legend.text.size` | change the font size of the legend body text. Defaults to `9`.
`facet.title.size` | change the font size of the facet wrap title text. Defaults to `10`.

### Value

An object created by `ggplot`

### Author(s)

Brandon Monier, brandon.monier@sdstate.edu

### Examples

    # Cuffdiff example
    data("df.cuff")
    vsVolcanoMatrix(
         data = df.cuff, d.factor = NULL, type = "cuffdiff",
         padj = 0.05, x.lim = NULL, lfc = 2, title = TRUE,
         grid = TRUE, counts = TRUE, data.return = FALSE
    )

    # DESeq2 example
    data("df.deseq")
    require(DESeq2)
    vsVolcanoMatrix(
         data = df.deseq, d.factor = "condition", type = "deseq",
         padj = 0.05, x.lim = NULL, lfc = 2, title = TRUE,
         grid = TRUE, counts = TRUE, data.return = FALSE
    )

    # edgeR example
    data("df.edger")
    require(edgeR)
    vsVolcanoMatrix(
         data = df.edger, d.factor = NULL, type = "edger",
         padj = 0.05, x.lim = NULL, lfc = 2, title = TRUE,
         grid = TRUE, counts = TRUE, data.return = FALSE
    )

    # Extract data frame from visualization
    data("df.cuff")
    tmp <- vsVolcanoMatrix(
         data = df.cuff, d.factor = NULL,
         type = "cuffdiff", padj = 0.05, x.lim = NULL,
         lfc = 2, title = TRUE, grid = TRUE,
         counts = TRUE, data.return = TRUE
    )
    df_vmat <- tmp[[1]]
    head(df_vmat)

    # Show plot from object (see prior example for more details)
    tmp[[2]] ## or use tmp$plot

[Package vidger version 1.7.0 Index]