omu (version 1.1.2)

plot_volcano: Create a volcano plot

Description

Creates a volcano plot as ggplot2 object using the output of omu_summary

Usage

plot_volcano(
  count_data,
  column,
  size,
  strpattern,
  fill,
  sig_threshold,
  alpha,
  shape,
  color
)

Arguments

count_data

The output file from the omu_summary function.

column

The column with metadata you want to highlight points in the plot with, i.e. "Class"

size

Size of the points in the plot

strpattern

A character vector of levels of the column you want the plot to focus on, i.e. strpattern = c("Carbohydrates", "Organicacids")

fill

A character vector of colors you want your points to be. Must be of length 1 + length(strpattern) to account for points not in strpattern. Levels of a factor are organzed alphabetically. All levels not in the strpattern argument will be set to NA.

sig_threshold

An integer. Creates a horizontal dashed line for a significance threshold. i.e. sig_threshold = 0.05. Defaut value is 0.05

alpha

A character vector for setting transparency of factor levels.Must be of length 1 + length(strpattern) to account for points not in strpattern.

shape

A character vector for setting the shapes for your column levels. Must be of length 1 + length(strpattern) to account for points not in strpattern. See ggplot2 for an index of shape values.

color

A character vector of colors for the column levels. Must be of length 1 + length(strpattern) to account for points not in strpattern. If you choose to use shapes with outlines, this list will set the outline colors.

Examples

c57_nos2KO_mouse_countDF <- assign_hierarchy(c57_nos2KO_mouse_countDF, TRUE, "KEGG")
c57_nos2KO_mouse_countDF <- c57_nos2KO_mouse_countDF[1:20,]
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")

plot_volcano(count_data = t_test_df, column = "Class", strpattern = c("Carbohydrates"),
fill = c("firebrick2", "white"), sig_threshold = 0.05, alpha = c(1,1),
shape = c(1,24), color = c("black", "black"), size = 2)

plot_volcano(count_data = t_test_df, sig_threshold = 0.05, size = 2)