scatplot.log2: Scatter plot of two columns of a data.frame after log2...
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

scatplot.log2

R Documentation

Scatter plot of two columns of a data.frame after log2 transformation.

Description

Scatter plot of two columns of a data.frame after log2 transformation.

Usage

scatplot.log2(data, x, y, title = "", xlabs, ylabs, min, max, a = 0.65,
  xcor = 3.3, ycor = 16.999, binx = 0.2, biny = 0.2,
  methodcor = "all", usecor = "pairwise.complete.obs", dens = TRUE,
  rug = TRUE, geomsize = 2, fig = "all", scaleCol, verbose = FALSE,
  smooth = TRUE, smoothMethod = "gam",
  smoothFormula = as.formula("y ~ s(x, bs = 'cs')"), xmin, ymin, xmax,
  ymax, abline = TRUE, publi = TRUE, col = NULL, labCol,
  family = "", policeSize = 11, sizeLegend = 8, sizeCor = 3,
  dealWithSpace = FALSE, p2alpha = 1, p3alpha = 1)

Arguments

`data`	numeric data.frame
`x`	column name to be mapped to the x-axis
`y`	column name to be mapped to the y-axis
`title`	plot title
`xlabs`	x-axis title
`ylabs`	y-axis title
`min`	numeric, minimum of both x-axis and y-axis
`max`	numeric, maximum of both x-axis and y-axis
`a`	numeric, alpha scaling factor to apply to the data
`xcor`	numeric, x coordinate for the correlation annotation to be anchored on its center
`ycor`	numeric, y coordinate for the correlation annotation to be anchored
`binx`	numeric, bin to use for the marginal plot of the x-axis
`biny`	numeric, bin to use for the marginal plot of the y-axis
`methodcor`	'all' for both Spearman and Pearson or or 'spearman' or 'pearson'
`usecor`	an optional character string giving a method for computing the correlation in the presence of missing values. This must be (an abbreviation of) one of the strings "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs" (default).
`dens`	logical, default TRUE. Whether density countour curves should be added to the main figure
`rug`	logical, default TRUE. Whether a rug should be added on the main figure
`geomsize`	numeric, default 2. the size of the geom_point()
`fig`	character string to chose from a set of predefined options that allows different outputs 'all' : complete figure with annotation and marginal plots 'grob': list of the grobs use by gridExtra::arrangeGrob to create the plot 'list': list of the different plots 'p' : the main figure with the legend 'p1' : the main figure without the legend 'p2' : the marginal figure on the x-axis 'p3' : the marginal figure on the y-axis 'legend': the legend of the figure only
`scaleCol`	colour palette to use for the plot
`verbose`	logical; default FALSE
`smooth`	logical; default TRUE whether a smooth curve should be plotted
`smoothMethod`	string, method to use for the smoothing default: "gam" (from mgcv package)
`smoothFormula`	formula to use with the smooth method default: as.formula("y ~ s(x, bs = 'cs')")
`xmin`	numeric, minimum of the x-axis
`ymin`	numeric, minimum of the y-axis
`xmax`	numeric, maximum of the x-axis
`ymax`	numeric, maximum of the y-axis
`abline`	logical; default: TRUE; whether the line y=x should be added as a reference
`publi`	logical, default: TRUE; whether to apply the theme_bw which is better suited for publication
`col`	colour palette
`labCol`	title for the colour scale
`family`	police family to use for the labels and titles
`policeSize`	base size for the plot
`sizeLegend`	size of the legend
`sizeCor`	size of the correlation annotation; default: 3
`dealWithSpace`	logical; default FALSE. Whether the space in the names of the columns to be plotted should be removed.
`p2alpha`	alpha scale for the marginal plot on the x-axis
`p3alpha`	alpha scale for the marginal plot on the y-axis