drLumi (version 0.1.2)

plot.scluminex: Plot method for the scluminex class

Description

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

Usage

"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

Value

A ggplot object

Details

All information in order to generate the plots is extracted from the scluminex 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")