MWAS_barplot: Visualize MWAS results in a bar plot

Description Usage Arguments Value Examples

View source: R/MWAS_visualization.R

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

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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

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## 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.