MWAS_skylineNMR: Visualize MWAS results in an NMR-skyline plot

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

Description

This function generates a 2-panel figure showing the results from "MWAS_stats()" applied to NMR data. The upper panel shows an NMR-skyline plot (comparable to a GWAS-Manhattan plot), where the chemical shifts are displayed along the x-axis and the -log10 p-values (sign-adjusted for the direction of the association) are displayed on the y-axis. The lower panel shows an NMR spectrum colored according to MWAS results.

Usage

MWAS_skylineNMR (metabo_SE, MWAS_matrix, ref_sample, alpha_th = 0.05, output = "all",
                 xlab ="ppm", ylab1 = "sign*log(pFDR)", ylab2 = "intensity", pch = 20,
                 marker_size = 1, scale_color = c("black", "cornflowerblue", "red"),
                 size_lab = 12, size_axis = 12, xlim = NULL, ylim1 = NULL,
                 ylim2 = NULL, guide_type = "legend", xbreaks = waiver(),
                 xnames = waiver(), ybreaks1 = waiver(), ybreaks2 = waiver(),
                 ynames1 = waiver(), ynames2 = waiver())

Arguments

metabo_SE	SummarizedExperiment object. See "MWAS_SummarizedExperiment()".
MWAS_matrix	numeric matrix resulting from the function "MWAS_stats()".
ref_sample	character vector indicating the ID of the sample that will be used to plot the NMR spectrum.
alpha_th	numeric value indicating the significance threshold.
output	character constant indicating the outcome of the function ("skyline", "spectrum" or "all"). If outcome = "all", both the skyline and the spectrum with be plotted in a 2-panel plot.
xlab	character vector specifying a title for the x-axis.
ylab1	character vector specifying a title for the y-axis of the upper panel.
ylab2	character vector specifying a title for the y-axis of the lower panel.
pch	value specifying the symbol used to represent each ppm value in the skyline plot. To see all possible symbols, check "plot()" options.
marker_size	numeric value indicating the size of the symbol used to represent each ppm value in the skyline plot.
scale_color	character vector corresponding to the 3-color scale that will be used to represent the association results. The first color of the scale indicates "no change", the second color indicates "downregulation", and the third color indicates "upregulation".
size_lab	numeric value indicating the font size of x- and y-axis titles.
size_axis	numeric value indicating the font size of x- and y-axis labels.
xlim	numeric vector containing the minimum and maximum values of the x-axis. Notice that ppm is displayed in reverse scale (e.g. xlim = c(5, 2)).
ylim1	numeric vector containing the minimum and maximum values of the y-axis for the upper panel.
ylim2	numeric vector containing the minimum and maximum values of the y-axis for the lower panel.
guide_type	character constant indicating the guide ("legend" or "none") that will be added to the plots.
xbreaks	numeric vector indicating the positions of the breaks of the x-axis.
xnames	character vector (same length as xbreaks) containing the labels of each break of the x-axis.
ybreaks1	numeric vector indicating the positions of the breaks of the y-axis for the upper panel.
ybreaks2	numeric vector indicating the positions of the breaks of the y-axis for the lower panel.
ynames1	character vector (same length as ybreaks1) containing the labels of each break of the y-axis for the upper panel.
ynames2	character vector (same length as ybreaks2) containing the labels of each break of the y-axis for the lower panel.

Value

By default, a plot with 2 panels, the upper panel showing an NMR-skyline plot and the lower panel showing an NMR spectrum colored based on MWAS results.

References

Elliott P, et al. (2015). Urinary metabolic signatures of human adiposity. Science Translational Medicine, 7, 285ra62.

Examples

## Load data
data(metabo_SE)

## Test for association between BMI and metabolic_data
BMI_model <- MWAS_stats (metabo_SE, disease_id = "BMI", assoc_method = "spearman",
                         output = "pvalues")

## Create skyline plots
MWAS_skylineNMR (metabo_SE, BMI_model, ref_sample = "QC1")
MWAS_skylineNMR (metabo_SE, BMI_model, ref_sample = "QC1", pch = "*", marker_size = 3)

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