verboseScatterplot: Scatterplot annotated by regression line and p-value

Description Usage Arguments Details Value Author(s) See Also

View source: R/Functions.R

Description

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

Usage

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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,
                   ...)

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.

...

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. 11, 2018, 9:03 a.m.