plot_heatmap {lipidr} | R Documentation

## Plot an annotated heatmap Plots a hierarchically clustered heatmap showing selected sample and lipid molecule annotations.

### Description

Plot an annotated heatmap Plots a hierarchically clustered heatmap showing selected sample and lipid molecule annotations.

### Usage

    plot_heatmap(
      data,
      measure = "Area",
      molecule_annotation = "Class",
      sample_annotation = "all",
      cluster_cols = "hclust",
      cluster_rows = "hclust",
      scale = "rows",
      ...
    )

### Arguments

`data` | LipidomicsExperiment object.
`measure` | Which measure to plot the distribution of: usually Area, Area Normalized, Height or Retention Time. Default is `Area`.
`molecule_annotation` | The column name for lipid annotation, default to `Class`.
`sample_annotation` | The column name for sample annotation, default to `all`.
`cluster_cols` | "none","hclust", or "k-means" for no clustering, hierarchical clustering, and k-means clustering of rows respectively. Default is "hclust".
`cluster_rows` | "none","hclust", or "k-means" for no clustering, hierarchical clustering, and k-means clustering of rows respectively. Default is "hclust".
`scale` | character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "cols" and "none".
`...` | Additional parameters passed to `iheatmapr::iheatmap()`.

### Value

A heatmap plot

### Examples

    data(data_normalized)
    plot_heatmap(data_normalized, sample_annotation = "group")

[Package lipidr version 2.8.1 Index]