present.cdf.3d: Generates 3 dimensional plots for LCMS data.

View source: R/present.cdf.3d.R

present.cdf.3dR Documentation

Generates 3 dimensional plots for LCMS data.

Description

This function takes the matrix output from proc.cdf() and generates a 3D plot of the data. It relies on the rgl library.

Usage

present.cdf.3d(prof, fill.holes = TRUE, transform = "none", time.lim = NA, mz.lim = NA, box = TRUE, axes = TRUE)

Arguments

prof

The matrix output from the proc.cdf() function.

fill.holes

A lot of peaks have missing values at some time points. If fill.holes is TRUE, the function will fill in the missing values by interpolation.

transform

If the value is "sqrt", the values are transformed by taking square root. If "cuberoot", the values are transformed by taking cubic root.

time.lim

The limit in retention time for the area of spectrum to be plotted. It should be either NA or a vector of two values: the lower limit and the upper limit.

mz.lim

The limit in m/z value for the area of spectrum to be plotted. It should be either NA or a vector of two values: the lower limit and the upper limit.

box

If a box should be drawn.

axes

If the axes should be drawn.

Details

The function calls the rgl library. Spectrum values within the time.lim and mz.lim range is plotted in 3D.

Value

There is no return value from this function.

Author(s)

Tianwei Yu <tyu8@emory.edu>

References

http://rgl.neoscientists.org/about.shtml

Examples

data(prof)
present.cdf.3d(prof[[2]],time.lim=c(250,400), mz.lim=c(400,500))

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