omu (version 1.1.2)

plot_heatmap: Create a heatmap

Description

Takes a metabolomics count data frame and creates a heatmap. It is recommended to either subset, truncate, or agglomerate by metabolite metadata to improve legibility.

Usage

plot_heatmap(
  count_data,
  metadata,
  Factor,
  response_variable,
  log_transform = FALSE,
  high_color,
  low_color,
  aggregate_by
)

Arguments

count_data

A metabolomics count data frame.

metadata

The descriptive meta data for the samples.

Factor

The column name for the independent variable in your metadata.

response_variable

The response variable for the data, i.e. "Metabolite"

log_transform

TRUE or FALSE. Recommended for visualization purposes. If true data is transformed by the natural log.

high_color

Color for high abundance values

low_color

Color for low abundance values

aggregate_by

Hierarchical metadata value to sum metabolite values by, i.e. "Class"

Examples

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

plot_heatmap(count_data = c57_nos2KO_mouse_countDF, metadata = c57_nos2KO_mouse_metadata,
log_transform = TRUE, Factor = "Treatment", response_variable = "Metabolite",
aggregate_by = "Subclass_2", high_color = "darkgoldenrod1", low_color = "dodgerblue2")