R: Scatterplot annotated by regression line and p-value

verboseScatterplot {WGCNA}

R Documentation

Scatterplot annotated by regression line and p-value

Description

Produce a scatterplot annotated by the correlation, p-value, and regression line.

Usage

verboseScatterplot(x, y, 
                   sample = NULL,
                   corFnc = "cor", corOptions = "use = 'p'", 
                   main = "", xlab = NA, ylab = NA, 
                   cex = 1, cex.axis = 1.5, cex.lab = 1.5, cex.main = 1.5, 
                   abline = FALSE, abline.color = 1, abline.lty = 1,
                   corLabel = corFnc, 
                   displayAsZero = 1e-5,
                   col = 1, bg = 0, pch = 1,
                   lmFnc = lm,
                   plotPriority = NULL,
                   showPValue = TRUE,
                   ...)

Arguments

`x`	numerical vector to be plotted along the x axis.
`y`	numerical vector to be plotted along the y axis.
`sample`	determines whether `x` and `y` should be sampled for plotting, useful to keep the plot manageable when `x` and `y` are large vectors. The default `NULL` value implies no sampling. A single numeric value will be interpreted as the number of points to sample randomly. If a vector is given, it will be interpreted as the indices of the entries in `x` and `y` that should be plotted. In either case, the correlation and p value will be determined from the full vectors `x` and `y`.
`corFnc`	character string giving the correlation function to annotate the plot.
`corOptions`	character string giving further options to the correlation function.
`main`	main title for the plot.
`xlab`	label for the x-axis.
`ylab`	label for the y-axis.
`cex`	character expansion factor for plot annotations, recycled as necessary.
`cex.axis`	character expansion factor for axis annotations.
`cex.lab`	character expansion factor for axis labels.
`cex.main`	character expansion factor for the main title.
`abline`	logical: should the linear regression fit line be plotted?
`abline.color`	color specification for the fit line.
`abline.lty`	line type for the fit line.
`corLabel`	character string to be used as the label for the correlation value printed in the main title.
`displayAsZero`	Correlations whose absolute value is smaller than this number will be displayed as zero. This can result in a more intuitive display (for example, cor=0 instead of cor=2.6e-17).
`col`	color of the plotted symbols. Recycled as necessary.
`bg`	fill color of the plotted symbols (used for certain symbols). Recycled as necessary.
`pch`	Integer code for plotted symbols (see `link{plot.default}`). Recycled as necessary.
`lmFnc`	linear model fit function. Used to calculate the linear model fit line if `'abline'` is `TRUE`. For example, robust linear models are implemented in the function `rlm`.
`plotPriority`	Optional numeric vector of same length as `x`. Points with higher plot priority will be plotted later, making them more visible if points overlap.
`showPValue`	Logical: should the p-value corresponding to the correlation be added to the title?
`...`	other arguments to the function `plot`.

Details

Irrespective of the specified correlation function, the p-value is always calculated for pearson correlation.

Value

If sample above is given, the indices of the plotted points are returned invisibly.

Author(s)

Steve Horvath and Peter Langfelder