scatter_chart: Group scatter chart

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

Group scatter chart

Description

Plots a 2d scatter plot of the input data.

Usage

scatter_chart(
  xcol = 1,
  ycol = 2,
  points_to_label = "none",
  factor_name = "none",
  ellipse = "all",
  ellipse_type = "norm",
  ellipse_confidence = 0.95,
  label_filter = character(0),
  label_factor = "rownames",
  label_size = 3.88,
  ...
)

Arguments

xcol	(numeric, integer, character) The column name, or index, of data to plot on the x-axis. The default is 1.
ycol	(numeric, integer, character) The column name, or index, of data to plot on the y-axis. The default is 2.
points_to_label	(character) Points to label. Allowed values are limited to the following: "none": No samples labels are displayed. "all": The labels for all samples are displayed. "outliers": Labels for for potential outlier samples are displayed. The default is "none".
factor_name	(character) The name of a sample-meta column to use. The default is "none".
ellipse	(character) Plot ellipses. Allowed values are limited to the following: "all": Ellipses are plotted for all groups and all samples. "group": Ellipses are plotted for all groups. "none": Ellipses are not included on the plot. "sample": An ellipse is plotted for all samples (ignoring group). The default is "all".
ellipse_type	(character) Type of ellipse. Allowed values are limited to the following: "norm": Multivariate normal (p = 0.95). "t": Multivariate t (p = 0.95). The default is "norm".
ellipse_confidence	(numeric) The confidence level for plotting ellipses. The default is 0.95.
label_filter	(character) Labels are only plotted for the named groups. If zero-length then all groups are included. The default is character(0).
label_factor	(character) The column name of sample_meta to use for labelling samples on the plot. "rownames" will use the row names from sample_meta. The default is "rownames".
label_size	(numeric) The text size of labels. Note this is not in Font Units. The default is 3.88.
...	Additional slots and values passed to struct_class.

Value

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

Inheritance

A scatter_chart object inherits the following struct classes:

⁠[scatter_chart]⁠ >> ⁠[chart]⁠ >> ⁠[struct_class]⁠

Examples

M = scatter_chart(
      xcol = 1,
      ycol = 2,
      points_to_label = "none",
      factor_name = "V1",
      ellipse = "all",
      label_filter = character(0),
      label_factor = "rownames",
      label_size = 3.88,
      ellipse_type = "norm",
      ellipse_confidence = 0.95)

D = iris_DatasetExperiment()
C = scatter_chart(
        xcol = 'Petal.Width',
        ycol = 'Sepal.Width',
        factor_name = 'Species'
    )
chart_plot(C,D)

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