MWAS_barplot: Visualize MWAS results in a bar plot

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

Description

This function creates a bar plot based on the output from "MWAS_stats()". This function is designed to visualize MWAS results in the case of discrete metabolic variables (e.g. target GC/MS metabolites).

Usage

MWAS_barplot(MWAS_matrix, alpha_th = 0.05, width = NULL,
             scale_color = c("darkgray", "cornflowerblue", "firebrick1"),
             legend_labs =c("unchanged","downregulated","upregulated"),
             ylab = "sign*log(pFDR)", size_yaxis = 12, size_ylab = 12,
             size_names = 10, angle_names = 45, sort = TRUE)

Arguments

MWAS_matrix	numeric matrix resulting from the function "MWAS_stats()".
alpha_th	numeric value indicating the significance threshold.
width	numeric value indicating bar width.
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".
legend_labs	character vector containing the legend labels, according to scale_color.
ylab	character vector specifying a title for the y-axis.
size_yaxis	numeric value indicating the font size of y-axis title.
size_ylab	numeric value indicating the font size of y-axis labels.
size_names	numeric value indicating the font size of the metabolite ids displayed on the x-axis.
angle_names	numeric value indicating the angle in which the metabolite ids will be displayed on the x-axis.
sort	logical constant indicating whether the metabolites will be sorted based on MWAS results.

Value

A bar plot.

Examples

## Load data
data(targetMetabo_SE)

## Test for association between diabetes and target_metabolites
T2D_model <- MWAS_stats (targetMetabo_SE, disease_id = "T2D",
                         confounder_ids = c("Age", "Gender", "BMI"),
                         assoc_method = "logistic")

## Bar plot
MWAS_barplot(T2D_model)
MWAS_barplot(T2D_model, width = 0.7) # change bar width
MWAS_barplot(T2D_model, width = 0.7, angle_names = 90)

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