verboseIplot: Scatterplot with density

In WGCNA: Weighted Correlation Network Analysis

Scatterplot with density

Description

Produce a scatterplot that shows density with color and is annotated by the correlation, MSE, and regression line.

Usage

verboseIplot(
             x, y, 
             xlim = NA, ylim = NA, 
             nBinsX = 150, nBinsY = 150, 
             ztransf = function(x) {x}, gamma = 1, 
             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, showMSE = TRUE, ...)

Arguments

x	numerical vector to be plotted along the x axis.
y	numerical vector to be plotted along the y axis.
xlim	define the range in x axis
ylim	define the range in y axis
nBinsX	number of bins along the x axis
nBinsY	number of bins along the y axis
ztransf	Function to transform the number of counts per pixel, which will be mapped by the function in colramp to well defined colors. The user has to make sure that the transformed density lies in the range [0,zmax], where zmax is any positive number (>=2).
gamma	color correction power
sample	either a number of points to be sampled or a vector of indices input x and y for points to be plotted. Useful when the input vectors are large and plotting all points is not practical.
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.
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.
showMSE	logical: should the MSE be added to the main title?
...	other arguments to the function plot.

Details

Irrespective of the specified correlation function, the MSE is always calculated based on the residuals of a linear model.

Value

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

Note

This funtion is based on verboseScatterplot (Steve Horvath and Peter Langfelder), iplot (Andreas Ruckstuhl, Rene Locher) and greenWhiteRed(Peter Langfelder )

Author(s)

Chaochao Cai, Steve Horvath

See Also

image for more parameters

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