vsVolcanoMatrix: Volcano plot matrix from log_{2} fold changes and...
In btmonier/vidger: Create rapid visualizations of RNAseq data in R

Description Usage Arguments Value Author(s) Examples

This function allows you to extract necessary results-based data from either a DESeq2 object, edgeR object, or cuffdiff data frame to create a volcano plot (i.e. a scatter plot) of the negative log of the p-value versus the log of the fold change while implementing ggplot2 aesthetics for all possible combinations of treatments.

vsVolcanoMatrix(data, d.factor = NULL, type = c("cuffdiff", "deseq",
  "edger"), padj = 0.05, x.lim = NULL, lfc = NULL, title = TRUE,
  legend = TRUE, grid = TRUE, counts = TRUE, data.return = FALSE,
  xaxis.text.size = 9, yaxis.text.size = 9, xaxis.title.size = 10,
  yaxis.title.size = 10, main.title.size = 15, legend.text.size = 9,
  facet.title.size = 10)

`data`	a cuffdiff, DESeq2, or edgeR object.
`d.factor`	a specified factor; for use with DESeq2 objects only. Defaults to `NULL`
`type`	an analysis classifier to tell the function how to process the data. Must be either `cuffdiff`, `deseq`, or `edgeR`.
`padj`	a user defined adjusted p-value cutoff point. Defaults to `0.05`.
`x.lim`	set manual limits to the x axis. Defaults to `NULL`.
`lfc`	log fold change level for setting conditonals. If no user input is added (`NULL`), value defaults to `1`.
`title`	show title of plot. Defaults to `TRUE`.
`legend`	shows legend of plot. Defaults to `TRUE`.
`grid`	show major and minor axis lines. Defaults to `TRUE`.
`counts`	displays the number of differentially expressed genes for each treatment comparison. Defaults to `TRUE`.
`data.return`	returns data output of plot if set to `TRUE`. Defaults to `FALSE`.
`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`.
`legend.text.size`	change the font size of the legend body text. Defaults to `9`.
`facet.title.size`	change the font size of the facet wrap title text. Defaults to `10`.

An object created by ggplot

Brandon Monier, brandon.monier@sdstate.edu

# Cuffdiff example
data("df.cuff")
vsVolcanoMatrix(
     data = df.cuff, d.factor = NULL, type = "cuffdiff",
     padj = 0.05, x.lim = NULL, lfc = 2, title = TRUE,
     grid = TRUE, counts = TRUE, data.return = FALSE
)

# DESeq2 example
data("df.deseq")
require(DESeq2)
vsVolcanoMatrix(
     data = df.deseq, d.factor = "condition", type = "deseq",
     padj = 0.05, x.lim = NULL, lfc = 2, title = TRUE,
     grid = TRUE, counts = TRUE, data.return = FALSE
)

# edgeR example
data("df.edger")
require(edgeR)
vsVolcanoMatrix(
     data = df.edger, d.factor = NULL, type = "edger",
     padj = 0.05, x.lim = NULL, lfc = 2, title = TRUE,
     grid = TRUE, counts = TRUE, data.return = FALSE
)

# Extract data frame from visualization
data("df.cuff")
tmp <- vsVolcanoMatrix(
     data = df.cuff, d.factor = NULL,
     type = "cuffdiff", padj = 0.05, x.lim = NULL,
     lfc = 2, title = TRUE, grid = TRUE,
     counts = TRUE, data.return = TRUE
)
df_vmat <- tmp[[1]]
head(df_vmat)

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