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)

### 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.

### 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
    )

[Package vidger version 1.0.0 Index]