plot,metabCombiner,ANY-method {metabCombiner} | R Documentation

## 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

[Package metabCombiner version 1.2.2 Index]