EIC.plot: Plot extracted ion chromatograms

View source: R/EIC.plot.R

EIC.plotR Documentation

Plot extracted ion chromatograms

Description

Given an output object from the function cdf.to.ftr(), this function plots the EICs selected by the user.

Usage

EIC.plot(aligned, rows = NA, colors = NA, transform = "none",
                 subset = NA, min.run, min.pres, max.spline.time.points
                 = 1000)

Arguments

aligned

An output object from cdf.to.ftr().

rows

A numeric vector selecting which rows of the aligned feature table to be plotted.

colors

The colors (one per profile) the user wishes to use for the plots. The default is NA, in which case a default color set is used.

transform

There are four possible values. "none": the original intensity data is plotted; "log": the intensity data is transformed by log(x+1); "sqrt": the intensity data is square root transformed; "cuberoot": the intensity data is cube root transformed.

subset

The user can choose a subset of the profiles for which the EICs are plotted. It is given as a vector of profile indecies. The default is NA, in which case the EICs from all the profiles are plotted.

min.run

The min.run parameter used in the proc.cdf() step.

min.pres

The min.pres parameter used in the proc.cdf() step.

max.spline.time.points

The maximum time points to use in spline fit.

Details

The EICs are plotted as overlaid line plots. The graphic device is divided into four parts, each of which is used to plot one EIC. When all four parts are occupied, the function calls x11() to open another graphic device. The colors used (one per profile) is printed in the command window.

Value

There is no return value.

Author(s)

Tianwei Yu <tyu8@emory.edu>

References

Bioinformatics. 25(15):1930-36. BMC Bioinformatics. 11:559.


yufree/apLCMS documentation built on May 19, 2024, 1:22 p.m.