plot.scluminex: Plot method for the scluminex class

In drLumi: Multiplex Immunoassays Data Analysis

Description

This function takes a scluminex object and creates a standard curve, residuals or QQ-plot using ggplot2 package.

Usage

## S3 method for class 'scluminex'
plot(x, type = "scurve", subset.list = NULL,
    psize = 1.8, ncol = NULL, nrow = NULL, out.limit = 2.5,
    size.text = 1.5, size.legend = 2.5, interval = "confidence",
    level = 0.95, color.bkg = "green", ...)

Arguments

x	an object of class scluminex
type	character describing the type of plot ('scurve','residuals' or 'qqplot'). Default 'scurve'.
subset.list	list of analytes to be plotted. Default all analytes.
psize	numeric point size
ncol	number of columns to plot the analytes.
nrow	number of rows to plot the analytes.
out.limit	value that defines an outlier. Must be positive value. Only applies for type 'residuals'.
size.text	value that defines the size of the well into the residuals plot. Only applies for type 'residuals'.
size.legend	size of the legend. NA for not showing. Only applies for type 'scurve'.
interval	'confidence' or 'prediction' character in order to plot the fit and the corresponding bands. If NULL only observed points are plotted. Only applies for type 'scurve'.
level	confidence level for the interval. Default 0.95, only applies for type 'scurve'.
color.bkg	character specifying the color of the background line. NA for not showing background. Only applies for type 'scurve'.
...	other arguments to be passed to ggplot function

Details

All information in order to generate the plots is extracted from the scluminex object.

Value

A ggplot object

Examples

# Load data and estimate models
data(ecdata)
data(mfidata)

dat <- mfidata[mfidata$plate=="plate_1" & mfidata$analyte=="FGF",]

sdf <- data_selection(dat, ecdata)[[1]]
sdf_luminex <- scluminex("plate_1",sdf$standard, sdf$background,
"SSl4", bkg="ignore", fmfi="mfi", verbose=FALSE)

# Plot standard curves
plot(sdf_luminex, "sc")

# Plots residuals
plot(sdf_luminex, "res")

# Plot QQplot
plot(sdf_luminex, "qq")

Example output

drLumi documentation built on May 2, 2019, 2:45 p.m.