feature_profile_array: 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_array(
  run_order,
  qc_label,
  qc_column,
  colour_by,
  feature_to_plot,
  nrow = 5,
  log = TRUE,
  ...
)

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.
nrow	(numeric, integer) The number of rows in the plot. The default is 5.
log	(logical) Log transform. Allowed values are limited to the following: "TRUE": The data is log tranformed before plotting. "FALSE": The data is not transformed before plotting. The default is TRUE.
...	Additional slots and values passed to struct_class.

Value

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

Inheritance

A feature_profile_array object inherits the following struct classes:

⁠[feature_profile_array]⁠ >> ⁠[chart]⁠ >> ⁠[struct_class]⁠

Examples

M = feature_profile_array(
      run_order = character(0),
      qc_label = character(0),
      qc_column = character(0),
      colour_by = character(0),
      feature_to_plot = numeric(0),
      nrow = 1,
      log = FALSE)

D = MTBLS79_DatasetExperiment()
C = feature_profile_array(
    run_order='run_order',
    qc_label='QC',
    qc_column='Class',
    colour_by='Class',
    feature_to_plot=1:3,
    nrow=1,
    log=TRUE)
chart_plot(C,D)

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