plot_heatmap: Create a heatmap

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

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")

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