vsMAMatrix {vidger} | R Documentation

## MA plot matrix from log2 fold changes and -log10(p-values)

### Description

This function allows you to generate MA plots for all possible treatment combinations for a given factor in either a cuffdiff, DESeq2, or edgeR data set.

### Usage

    vsMAMatrix(data, d.factor = NULL, type = c("cuffdiff", "deseq", "edger"),
      padj = 0.05, y.lim = NULL, lfc = NULL, title = TRUE, legend = TRUE,
      grid = TRUE, counts = TRUE, data.return = FALSE)

### 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.
`padj` | a user defined adjusted p-value cutoff point. Defaults to '0.05'.
`y.lim` | set manual limits (boundaries) to the y axis. Defaults to 'NULL'.
`lfc` | log fold change level for setting conditonals. If no user input is added ('NULL'), value defaults to '1'.
`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.
`counts` | displays the number of differentially expressed genes for each treatment comparison. Defaults to 'TRUE'.
`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.

### Value

An object created by `ggplot`

### Author(s)

Brandon Monier, brandon.monier@sdstate.edu

### Examples

    # Cuffdiff example
    data("df.cuff")
    vsMAMatrix(
     data = df.cuff, d.factor = NULL, type = 'cuffdiff',
     padj = 0.05, y.lim = NULL, lfc = 1, title = TRUE,
     grid = TRUE, counts = TRUE, data.return = FALSE
    )

    # DESeq2 example
    data("df.deseq")
    require(DESeq2)
    vsMAMatrix(
     data = df.deseq, d.factor = 'condition', type = 'deseq',
     padj = 0.05, y.lim = NULL, lfc = 1, title = TRUE,
     grid = TRUE, counts = TRUE, data.return = FALSE
    )

    # edgeR example
    data("df.edger")
    require(edgeR)
    vsMAMatrix(
     data = df.edger, d.factor = NULL, type = 'edger',
     padj = 0.05, y.lim = NULL, lfc = 1, title = TRUE,
     grid = TRUE, counts = TRUE, data.return = FALSE
    )

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

[Package vidger version 1.0.0 Index]