vsDEGMatrix: Differential gene expression matrix
In vidger: Create rapid visualizations of RNAseq data in R

Description Usage Arguments Value Author(s) Examples

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.

vsDEGMatrix(data, padj = 0.05, d.factor = NULL, type = c("cuffdiff",
  "deseq", "edger"), title = TRUE, legend = TRUE, grid = TRUE,
  data.return = FALSE, grey.scale = FALSE, xaxis.text.size = 10,
  yaxis.text.size = 10, main.title.size = 15, legend.text.size = 10,
  legend.title.size = 12)

`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.
`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.
`grey.scale`	displays grey color scheme instead of blue if set to `TRUE`. Logical; defaults to `FALSE`.
`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`.
`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`.

An object created by ggplot

Brandon Monier, brandon.monier@sdstate.edu

# 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
)

# Extract data frame from visualization
data("df.edger")
require(edgeR)
tmp <- vsDEGMatrix(
     df.edger, padj = 0.05, d.factor = NULL, type = "edger",
     title = TRUE, legend = TRUE, grid = TRUE
)
df_deg <- tmp[[1]] ## or use tmp$data
head(df_deg)

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