plot_fit: Plot metabCombiner Fits

In hhabra/Combiner: Method for Combining LC-MS Metabolomics Feature Measurements

Plot metabCombiner Fits

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 = "black",
  lcol = "red",
  lwd = 3,
  pch = 19,
  outlier = "show",
  ocol = "springgreen4",
  legend = c("anchor", "outlier"),
  ...
)

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 normal points (ordered RT pair) in the plot
lcol	color of the fitted line in the plot
lwd	line width of the curve fit between anchor points
pch	plot character type; see ?graphics::par for details
outlier	display option for outliers. If "show" or "s", treats outlier points like normal anchors; if "remove" or "r", removes outlier points from the plot; if "highlight" or "h", displays outliers with a different color and associated legend.
ocol	color of the outlier points; outlier argument must be set to "highlight" or "h"
legend	length-2 character vector indicating point labels in the legend if outlier argument set to "highlight" or "h"

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, family = "gaussian")

##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", outliers = "remove")

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

hhabra/Combiner documentation built on Sept. 13, 2022, 11:34 a.m.