R: Scatter plot matrix of log_{10}(FPKM or CPM) values

vsScatterMatrix {vidger}

R Documentation

Scatter plot matrix of log_{10}(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,
  data.return = FALSE, xaxis.text.size = 9, yaxis.text.size = 9,
  xaxis.title.size = 10, yaxis.title.size = 10, main.title.size = 15,
  facet.title.size = 10)

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`.
`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 `9`.
`yaxis.text.size`	change the font size of the `y`-axis text. Defaults to `9`.
`xaxis.title.size`	change the font size of the `x`-axis title text. Defaults to `10`.
`yaxis.title.size`	change the font size of the `y`-axis title text. Defaults to `10`.
`main.title.size`	change the font size of the plot title text. Defaults to `15`.
`facet.title.size`	change the font size of the facet wrap title text. Defaults to `10`.

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
)

# Extract data frame from visualization
data("df.edger")
tmp <- vsScatterMatrix(
     data = df.edger, d.factor = NULL, type = "edger",
     comp = c("WM", "MM"), title = TRUE, grid = TRUE,
     man.title = NULL, data.return = TRUE
)
df_scatmat <- tmp[[1]] ## or use tmp$data
head(df_scatmat)

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

[Package vidger version 1.2.1 Index]