Add contour lines to cyto_plot

cyto_plot_contour(x, ...)

# S3 method for flowFrame
cyto_plot_contour(
  x,
  channels,
  contour_lines = 15,
  contour_line_type = 1,
  contour_line_width = 1,
  contour_line_col = "black",
  contour_line_alpha = 1,
  ...
)

# S3 method for flowSet
cyto_plot_contour(
  x,
  channels,
  contour_lines = 15,
  contour_line_type = 1,
  contour_line_width = 1,
  contour_line_col = "black",
  contour_line_alpha = 1,
  ...
)

# S3 method for list
cyto_plot_contour(
  x,
  channels,
  contour_lines = 15,
  contour_line_type = 1,
  contour_line_width = 1,
  contour_line_col = "black",
  contour_line_alpha = 1,
  ...
)

Arguments

x

either an object of class flowFrame, or flowSet or a list of flowFrame objects.

...

not in use.

channels

channels used to construct the existing cyto_plot.

contour_lines

numeric indicating the number of levels to use for contour lines, set to 15 by default.

contour_line_type

type of line to use for contour lines, set to 1 by default.

contour_line_width

line width for contour lines, set to 1 by default.

contour_line_col

colour to use for contour lines, set to "black" by default.

contour_line_alpha

numeric [0,1] to control transparency of contour lines, set to 1 by default to remove transparency.

Author

Dillon Hammill, Dillon.Hammill@anu.edu.au

Examples

library(CytoExploreRData) # Load in Samples fs <- Activation # Apply compensation fs <- cyto_compensate(fs) # Transform fluorescent channels trans <- cyto_transformer_logicle(fs)
fs <- cyto_transform(fs, trans)
# Plot cyto_plot(fs[[32]], channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"), axes_trans = trans )
# Contour lines cyto_plot_contour(fs[[32]], channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"), contour_lines = 20 )