verboseScatterplot: Scatterplot annotated by regression line and p-value

In WGCNA: Weighted Correlation Network Analysis

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

See Also

plot.default for standard scatterplots

WGCNA documentation built on Sept. 18, 2024, 5:08 p.m.