Plot dimensional reduction results

Visualizes dimensional reduction in a scatterplot.

plotPca(
  object,
  variable_set,
  phase = NULL,
  color_by = NULL,
  color_aes = "fill",
  pt_clrp = NULL,
  pt_clrsp = NULL,
  pt_alpha = NULL,
  pt_clr = NULL,
  pt_fill = NULL,
  pt_size = NULL,
  clrp_adjust = NULL,
  add_ons = list(ggplot2::labs(fill = NULL, color = NULL)),
  ...
)

plotTsne(
  object,
  variable_set,
  phase = NULL,
  color_by = NULL,
  color_aes = "fill",
  pt_clrp = NULL,
  pt_clrsp = NULL,
  pt_alpha = NULL,
  pt_clr = NULL,
  pt_fill = NULL,
  pt_size = NULL,
  clrp_adjust = NULL,
  add_ons = list(ggplot2::labs(fill = NULL, color = NULL)),
  ...
)

plotUmap(
  object,
  variable_set,
  phase = NULL,
  color_by = NULL,
  color_aes = "fill",
  pt_clrp = NULL,
  pt_clrsp = NULL,
  pt_alpha = NULL,
  pt_clr = NULL,
  pt_fill = NULL,
  pt_size = NULL,
  clrp_adjust = NULL,
  add_ons = list(ggplot2::labs(fill = NULL, color = NULL)),
  ...
)

Arguments

object	A valid cypro object.
variable_set	Character value. Denotes the variable set of interest. Use getVariableSetNames() to obtain all names of currently stored variable sets in your object.
phase	Character or numeric. If character, the ordinal value referring to the phase of interest (e.g. 'first', 'second' etc.). referring to the phase of interest or 'all'. If numeric, the number referring to the phase. If set to NULL takes the phase denoted as default with adjustDefault(). Ignored if the experiment design contains only one phase.
color_by	Character value or NULL. If character, denotes either the numeric- or grouping variable whoose values are displayed by color. If set to NULL the color is specified by the argument pt_clr.
color_aes	Character value. Only relevant if color_by is specified. Denotes the aesthetic with which colors are displayed. Either 'color' or 'fill'. Depending on that as well as the input for argument pt_shape the design of the geometric objects (points) varies according to the rules of the ggplot2-framework.
pt_clrp	The color palette to be used if the specified variable displayed by color is categorical/discrete. Run validColorPalettes() to see valid input.
pt_clrsp	The color spectrum to be used if the specified variable displayed by color is continuous. Run validColorSpectra() to see valid input.
pt_alpha	Numeric value. Specifies the degree of transparency of all points.
pt_clr	Character value. Specifies the color of all points.
pt_size	Numeric value. Specifies the size of all points.
clrp_adjust	Named character vector or NULL. If character, it adjusts the color palette that is used to represent the groups. Names of the input vector must refer to the group and the respective named element denotes the color with which to represent the group.

Value

A ggplot.