plot_heatmap: Plot an annotated heatmap Plots a hierarchically clustered...

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plot_heatmapR 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")

ahmohamed/lipidr documentation built on Aug. 17, 2022, 1:35 a.m.