density_plot: Wrapper around gpplot2's density plot with preset arguments
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

density_plot

R Documentation

Wrapper around gpplot2's density plot with preset arguments

Description

Wrapper around gpplot2's density plot with preset arguments

Usage

density_plot(DF, log2 = TRUE, pseudocount = 0, valueLab = "PSM",
  baseFont = "Linux Libertine", condCol, fontSize = 11,
  publish = TRUE, xmin, xmax, ymin, ymax, removeLegend = FALSE, thm,
  alphaScale = 0.2, ylab)

Arguments

`DF`	numeric data.frame containing expresion data
`log2`	boolean; default: TRUE. Whether a log2 transformation should be applied to the values
`pseudocount`	numeric. default: 0. Whether a pseudocount should be added before the log2 transformation is applied.
`valueLab`	character string representing the unit in which the gene expression is measured; added
`baseFont`	string character. Name of the font to use for the plot. Default: "Linux Libertine"
`condCol`	character string vector. Colour palette for the plot. The vector's names are for the conditions associated to each colour (content of the vector)
`fontSize`	font size. Default: 11.
`publish`	boolean. Default: TRUE. Whether to apply theme_bw() to the plot.
`xmin`	numeric. Lower limit for the x-axis.
`xmax`	numeric. Greater limitefor the x-axis.
`ymin`	numeric. Lower limit for the y-axis.
`ymax`	numeric. Greater limit for the y-axis.
`removeLegend`	boolean, default: FALSE. Whethere to remove the legend
`thm`	function theme( ) with the list of additional elements to apply
`alphaScale`	new alpha level in [0,1]. Default: 0.2
`ylab`	character string. Label for the y-axis