plot_fit: Plot metabCombiner Fits

In metabCombiner: Method for Combining LC-MS Metabolomics Feature Measurements

Description

This is a plotting method for metabCombiner objects. It displays ordered pairs and a curve fit computed using fit_gam or fit_loess, using base R graphics.

Usage

## S4 method for signature 'metabCombiner,ANY'
plot(x, y, ...)

plot_fit(
  object,
  fit = c("gam", "loess"),
  pcol,
  lcol,
  lwd,
  remove.outliers = FALSE,
  ...
)

Arguments

x	metabCombiner object
y	...
...	Other variables passed into graphics::plot
object	metabCombiner object
fit	choice of model (either "gam" or "loess").
pcol	color of the points (ordered pairs) in the plot.
lcol	color of the fitted line in the plot
lwd	line width of the curve fit between anchor points
remove.outliers	logical, option to exclude outlier anchors in plot

Value

no values returned

Examples

data(plasma30)
data(plasma20)

p30 <- metabData(plasma30, samples = "CHEAR")
p20 <- metabData(plasma20, samples = "Red", rtmax = 17.25)
p.comb = metabCombiner(xdata = p30, ydata = p20, binGap = 0.0075)
p.comb = selectAnchors(p.comb, tolmz = 0.003, tolQ = 0.3, windy = 0.02)
p.comb = fit_gam(p.comb, k = 20, iterFilter = 1)

##plot of GAM fit
plot(p.comb, main = "Example GAM Fit Plot", xlab = "X Dataset RTs",
     ylab = "Y Dataset RTs", pcol = "red", lcol = "blue", lwd = 5,
     fit = "gam", pch = 19, remove.outliers = TRUE)

grid(lwd =  2, lty = 3 ) #adding gridlines

metabCombiner documentation built on Dec. 10, 2020, 2 a.m.