vsBoxPlot {vidger} | R Documentation

## Box plot for log_{10}(FPKM or CPM) distributions

### Description

This function allows you to extract necessary results-based data from analytical objects to create a box plot comparing log10(FPKM or CPM) distributions for experimental treatments.

### Usage

    vsBoxPlot(data, d.factor = NULL, type = c("cuffdiff", "deseq", "edger"),
      title = TRUE, legend = TRUE, grid = TRUE, aes = c("box", "violin",
      "boxdot", "viodot", "viosumm", "notch"), fill.color = NULL,
      data.return = FALSE, xaxis.text.size = 10, yaxis.text.size = 10,
      xaxis.title.size = 12, yaxis.title.size = 12, 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`.
`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.
`aes` | changes overall layout of the graph. `box`: box plot; `violin`: violin plot; `boxdot`: box plot with dots; `viodot`: violin plot with dots; `viosumm`: violin plot with summary statistics; `notch`: box plots with notches. Defaults to `box`.
`fill.color` | changes the fill color for the plots. See `RColorBrewer::display.brewer.all()` function for further details. If `NULL`, colors will default to standard `ggplot2` aesthetics.
`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.
`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`.
`xaxis.title.size` | change the font size of the `x`-axis title text. Defaults to `12`.
`yaxis.title.size` | change the font size of the `y`-axis title text. Defaults to `12`.
`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")
    vsBoxPlot(
         data = df.cuff, d.factor = NULL, type = "cuffdiff", title = TRUE,
         legend = TRUE, grid = TRUE
    )

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

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

    # Display different colors for plot
    data("df.edger")
    vsBoxPlot(
         data = df.edger, d.factor = NULL, type = "edger", title = TRUE,
         legend = TRUE, grid = TRUE, fill.color = "RdGy",
         data.return = FALSE
    )

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

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

[Package vidger version 1.6.0 Index]