QC_CV_scatterplot: Plot MS-based scatter plot colored based on CV

In MWASTools: MWASTools: an integrated pipeline to perform metabolome-wide association studies

Description

This function creates a MS-based scatter plot (rt vs mz) where the metabolic features are colored based on their coefficient of variation (CV). See "QC_CV()".

Usage

QC_CV_scatterplot (rt, mz, CV_metabo, CV_th = 0.30, xlab = "rt",
                   ylab = "mz", pch = 20, marker_size = 1, xlim = NULL,
                   ylim = NULL, size_axis = 10, size_lab = 10)

Arguments

rt	numeric vector of retention time values.
mz	numeric vector of mz values.
CV_metabo	numeric vector containing the CV of each metabolic feature. The length of this vector should be consistent with the length of rt and mz.
CV_th	numeric value indicating the CV threshold. NMR signals with CV equal or above CV_th will be colored in red.
xlab	character vector specifying a title for the x-axis.
ylab	character vector specifying a title for the y-axis.
pch	value specifying the symbol used to represent each MS feature in the scatter plot. To see all possible symbols, check "plot()" options.
marker_size	numeric value indicating the size of the symbol used to represent each metabolic feature in the scatter plot.
xlim	numeric vector containing the minimum and maximum values of the x-axis.
ylim	numeric vector containing the minimum and maximum values of the y-axis.
size_axis	numeric value indicating the font size of x- and y-axis title.
size_lab	numeric value indicating the font size of x- and y-axis labels.

Value

A MS-based scatter plot where MS features are represented according on CV.

Examples

## Load data
data(MS_data)
rt <- MS_data[, 1]
mz <- MS_data[, 2]

## Simulate CV values
CV_metabo <- runif(length(rt), 0.05, 0.31)

## MS-based scatter plot
QC_CV_scatterplot(rt, mz, CV_metabo)
QC_CV_scatterplot(rt, mz, CV_metabo, xlim = c(0, 10))
QC_CV_scatterplot(rt, mz, CV_metabo, CV_th = 0.15)

MWASTools documentation built on Nov. 8, 2020, 5:07 p.m.