plot_bar: Create a bar plot

In omu: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection

Create a bar plot

Description

Creates a ggplot2 object using the output file from the count_fold_changes function

Usage

plot_bar(fc_data, fill, size = c(1, 1), outline_color = c("black", "black"))

Arguments

fc_data	The output file from Count_Fold_Changes
fill	A character vector of length 2 containing colors for filling the bars, the first color is for the "Decrease" bar while the second is for "Increase"
size	A numeric vector of 2 numbers for the size of the bar outlines.
outline_color	A character vector of length 2 containing colors for the bar outlines

Examples

c57_nos2KO_mouse_countDF <- assign_hierarchy(c57_nos2KO_mouse_countDF, TRUE, "KEGG")

t_test_df <- omu_summary(count_data = c57_nos2KO_mouse_countDF,
metadata = c57_nos2KO_mouse_metadata, numerator = "Strep", denominator = "Mock",
response_variable = "Metabolite", Factor = "Treatment",
log_transform = TRUE, p_adjust = "BH", test_type = "welch")

fold_change_counts <- count_fold_changes(count_data = t_test_df,
column = "Class", sig_threshold = 0.05, keep_unknowns = FALSE)

plot_bar(fc_data = fold_change_counts, fill = c("firebrick2", "dodgerblue2"),
outline_color = c("black", "black"), size = c(1,1))

omu documentation built on Oct. 17, 2023, 1:06 a.m.