MWAS_scatterplotMS: Visualize MWAS results in MS-based scatter plot

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

Description

This function creates a MS-based scatter plot (rt vs mz) based on the output from "MWAS_stats()". MS-features are filtered according to a given significance threshold and only significant features are represented in the scatter plot. The color of the marker representing each significant MS feature indicates the direction of the association (i.e. downregulation or upregulation) and the size of the marker indicates the strength of the association (i.e. -log10(p-value)).

Usage

MWAS_scatterplotMS (rt, mz, MWAS_matrix, alpha_th = 0.05, xlab = "rt",
                    ylab = "mz", pch = 20, scale_color = c("cornflowerblue", "red"),
                    xlim = NULL, ylim = NULL, size_axis = 10, size_lab = 10,
                    legend_position = "bottom")

Arguments

rt	numeric vector of retention time values.
mz	numeric vector of mz values.
MWAS_matrix	numeric matrix resulting from the function "MWAS_stats()". The dimensions of this matrix must be consistent with the length of rt and mz
alpha_th	numeric value indicating the significance threshold. Only variables with p-value (corrected for multiple-testing) below alpha_th will be plotted.
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.
scale_color	character vector corresponding to the 2-color scale that will be used to represent the association results. The first color of the scale indicates "downregulation", and the second color indicates "upregulation".
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.
legend_position	character vector indicating the position of the legend: "top", "bottom", "right", "left", "none".

Value

A MS-based scatter plot where MS features are represented according to MWAS_results.

Examples

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

## Simulate MWAS data
set.seed(100)
estimates <- runif(length(rt), -1, 1)
pvalues <- rbeta(length(estimates), 0.5, 1)
pFDR <- p.adjust(pvalues, method = "BH")
MWAS_matrix <- cbind(estimates, pvalues, pFDR)

## MS-based scatter plot
MWAS_scatterplotMS(rt, mz, MWAS_matrix)
MWAS_scatterplotMS(rt, mz, MWAS_matrix, alpha_th = 0.01)
MWAS_scatterplotMS(rt, mz, MWAS_matrix, alpha_th = 0.01,
                  scale_color = c("yellow", "blue"))

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