feature_profile: Feature profile

In computational-metabolomics/structtoolbox: Data processing & analysis tools for Metabolomics and other omics

Feature profile

Description

A plot visualising the change in intensity of a feature with a continuous variable such as time, dose, or run order.

Usage

feature_profile(
  run_order,
  qc_label,
  qc_column,
  colour_by,
  feature_to_plot,
  plot_sd = FALSE,
  ...
)

Arguments

run_order	(character) The sample-meta column name containing run order.
qc_label	(character) The label used to identify QC samples.
qc_column	(character) The sample-meta column name containing the labels used to identify QC samples.
colour_by	(character) The sample-meta column name to used to colour the plot.
feature_to_plot	(numeric, character, integer) The name or column id of the plotted feature.
plot_sd	(logical) Plot standard deviation. Allowed values are limited to the following: "TRUE": Standard deviation of samples and QCs are included on the plot. "FALSE": Standard deviation is not plotted. The default is FALSE.
...	Additional slots and values passed to struct_class.

Value

A feature_profile object. This object has no output slots. See chart_plot in the struct package to plot this chart object.

Inheritance

A feature_profile object inherits the following struct classes:

⁠[feature_profile]⁠ >> ⁠[chart]⁠ >> ⁠[struct_class]⁠

Examples

M = feature_profile(
      run_order = character(0),
      qc_label = character(0),
      qc_column = character(0),
      colour_by = character(0),
      feature_to_plot = numeric(0),
      plot_sd = FALSE)

D = MTBLS79_DatasetExperiment()
C = feature_profile(run_order='run_order',
    qc_label='QC',
    qc_column='Class',
    colour_by='Class',
    feature_to_plot=1)
chart_plot(C,D)

computational-metabolomics/structtoolbox documentation built on Feb. 9, 2024, 8:19 a.m.