plot.features: Plot EIC

In HuanLab/JPA:

Plot EIC

Description

Plots the EICs of either level 1, 2, 3, target, or aligned features (multi-sample analysis).

Usage

plot.features(dir, featureTable, data, plot.type, plotmz.tol = 0.01, plotrt.tol = 60, smooth = 2)

Arguments

dir	Directory to save the plots to.
featureTable	Feature table dataframe generated in previous steps containing level information.
data	"MSdata" object generated in previous steps.
plot.type	The type of features to plot. 1 for level 1 features, 2 for level 2 features, 3, for level 3 features, "target" for target features, and "aligned" for aligned features in multi-sample analysis.
plotmz.tol	Mass range in dalton for plotting EIC. Default = 0.01.
plotrt.tol	Retention time range in seconds for plotting EIC. Default = 60.
smooth	Smoothing level for plotting EIC. Default = 2.

Value

Returns nothing, only plots all EICs of specified level to local disk.

Author(s)

Sam Shen, Jian Guo, Tao Huan

Examples

library(IPA)
dir = "X:/Users/Sam_Shen/IPAtest_20210330/singleDDA"
tarFTdir = "X:/Users/Sam_Shen/IPAtest_20210330"
tarFTname = "LibraryCSVHILIC-.csv"
featureTable <- peak.picking(dir = dir, mz.tol = 10, ppm=10, peakwidth=c(5,20), mzdiff = 0.01,
                             snthresh = 6, integrate = 1, prefilter = c(3,100), noise = 100)
featureTable <- find.level3features(data = MSdata)
featureTable <- add.targetfeatures(data = MSdata, tarFTdir = tarFTdir, tarFTname = tarFTname)

plotdir <- "X:/Users/Sam_Shen/IPAtest_20210330"
plot.features(dir = plotdir, featureTable = featureTable, data = MSdata, plot.type = 1, smooth = 2)
plot.features(dir = plotdir, featureTable = featureTable, data = MSdata, plot.type = 2, smooth = 2)
plot.features(dir = plotdir, featureTable = featureTable, data = MSdata, plot.type = 3, smooth = 2)
plot.features(dir = plotdir, featureTable = featureTable, data = MSdata, plot.type = "target", smooth = 2)

HuanLab/JPA documentation built on April 14, 2023, 12:53 p.m.