vsScatterMatrix {vidger} | R Documentation

## Scatter plot matrix of log10(FPKM or CPM) values

### Description

This function will generate a matrix of scatterplots for all possible treatment combinations with additional distribution info.

### Usage

    vsScatterMatrix(data, d.factor = NULL, type = c("cuffdiff", "deseq",
      "edger"), comp = NULL, title = TRUE, grid = TRUE, man.title = NULL)

### 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'.
`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.
`comp` | treatments you would like to compare in the form of a vector. If no parameter is specified, all possible treatment comparisons will be made. Defaults to 'NULL'.
`title` | display the main title of plot. Logical; defaults to 'TRUE'. If set to 'FALSE', no title 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.
`man.title` | a manually specified title at the authors discretion. Defaults to 'NULL'.

### Value

An object created by `ggplot`

### Author(s)

Brandon Monier, brandon.monier@sdstate.edu

### Examples

    # Cuffdiff example
    data("df.cuff")
    vsScatterMatrix(
     data = df.cuff, d.factor = NULL, type = 'cuffdiff',
     comp = NULL, title = TRUE, grid = TRUE,
     man.title = 'Example title'
    )

    # DESeq2 example
    data("df.deseq")
    require(DESeq2)
    vsScatterMatrix(
     data = df.deseq, d.factor = 'condition', type = 'deseq',
     comp = NULL, title = TRUE, grid = FALSE, man.title = NULL
    )

    # edgeR example
    data("df.edger")
    require(edgeR)
    vsScatterMatrix(
     data = df.edger, d.factor = NULL, type = 'edger',
     comp = c('WM', 'MM'), title = TRUE, grid = TRUE,
     man.title = NULL
    )

[Package vidger version 1.0.0 Index]