verboseIplot {WGCNA}

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