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Group scatter chart

Source: R/scatter_chart_class.R
scatter_chart.Rd

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)