MWAS_skylineNMR {MWASTools} | R Documentation

## Visualize MWAS results in an NMR-skyline plot

### 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)

[Package MWASTools version 1.4.0 Index]