vsDEGMatrix {vidger} | R Documentation

## Differential gene expression matrix

### Description

This function allows you to visualize the number of differentially expressed genes (DEG) at a given adjusted P-value for each experimental treatment level. Higher color intensity correlates to a higher number of DEGs.

### Usage

    vsDEGMatrix(data, padj = 0.05, d.factor = NULL, type = c("cuffdiff",
      "deseq", "edger"), title = TRUE, legend = TRUE, grid = TRUE,
      data.return = FALSE, grey.scale = FALSE, xaxis.text.size = 10,
      yaxis.text.size = 10, main.title.size = 15, legend.text.size = 10,
      legend.title.size = 12)

### Arguments

`data` | output generated from calling the main routines of either `cuffdiff`, `DESeq2`, or `edgeR` analyses. For `cuffdiff`, this will be a `*_exp.diff` file. For `DESeq2`, this will be a generated object of class `DESeqDataSet`. For `edgeR`, this will be a generated object of class `DGEList`.
`padj` | a user defined adjusted p-value cutoff point. Defaults to `0.05`.
`d.factor` | a specified factor; for use with `DESeq2` objects only. This input equates to the first parameter for the contrast argument when invoking the `results()` function in `DESeq2`. Defaults to `NULL`
`type` | an analysis classifier to tell the function how to process the data. Must be either `cuffdiff`, `deseq`, or `edger`. `cuffdiff` must be used with `cuffdiff` data; `deseq` must be used for `DESeq2` output; `edgeR` must be used with `edgeR` data. See the `data` parameter for further details.
`title` | display the main title of plot. Logical; defaults to `TRUE`. If set to `FALSE`, no title will display in plot.
`legend` | display legend of plot. Logical; defaults to `TRUE`. If set to `FALSE`, no legend will display in plot.
`grid` | display major and minor axis lines. Logical; defaults to `TRUE`. If set to `FALSE`, no axis lines will display in plot.
`data.return` | returns data output of plot. Logical; defaults to `FALSE`. If set to `TRUE`, a data frame will also be called. Assign to object for reproduction and saving of data frame. See final example for further details.
`grey.scale` | displays grey color scheme instead of blue if set to `TRUE`. Logical; defaults to `FALSE`.
`xaxis.text.size` | change the font size of the `x`-axis text. Defaults to `10`.
`yaxis.text.size` | change the font size of the `y`-axis 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 `10`.
`legend.title.size` | change the font size of the legend title text. Defaults to `12`.

### Value

An object created by `ggplot`

### Author(s)

Brandon Monier, brandon.monier@sdstate.edu

### Examples

    # cuffdiff example
    data("df.cuff")
    vsDEGMatrix(
         df.cuff, padj = 0.05, d.factor = NULL, type = "cuffdiff",
         title = TRUE, legend = TRUE, grid = TRUE
    )

    # DESeq2 example
    data("df.deseq")
    require(DESeq2)
    vsDEGMatrix(
         df.deseq, padj = 0.05, d.factor = "condition", type = "deseq",
         title = TRUE, legend = TRUE, grid = TRUE
    )

    # edgeR example
    data("df.edger")
    require(edgeR)
    vsDEGMatrix(
         df.edger, padj = 0.05, d.factor = NULL, type = "edger",
         title = TRUE, legend = TRUE, grid = TRUE
    )

    # Extract data frame from visualization
    data("df.edger")
    require(edgeR)
    tmp <- vsDEGMatrix(
         df.edger, padj = 0.05, d.factor = NULL, type = "edger",
         title = TRUE, legend = TRUE, grid = TRUE
    )
    df_deg <- tmp[[1]] ## or use tmp$data
    head(df_deg)

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

[Package vidger version 1.2.1 Index]