plot_mds: Plot the results from run_comparison as a two dimension...

In cannin/tumorcomparer: Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity

Plot the results from run_comparison as a two dimension multi-dimensional scaling (MDS) plot

Description

Plot the results from run_comparison as a two dimension multi-dimensional scaling (MDS) plot

Usage

plot_mds(
  comparison_result,
  categorization_list = NULL,
  trim_cell_line_names = FALSE,
  tumor_color = "blue",
  cell_line_color = "orange",
  use_gradient = FALSE,
  tumor_shape = 20,
  cell_line_shape = 17
)

Arguments

comparison_result	the results of run_comparison() (See: run_comparison())
categorization_list	the results of categorize_cell_lines() (See: categorize_cell_lines()). Default: NULL. Only necessary if to show a gradient on the MDS plot; disabled by default.
trim_cell_line_names	a boolean whether to trim the the cell lines; this is optional and used for long cell line names in CCLE format (i.e. CELLLINE_TISSUE)
tumor_color	a color for tumor points (DEFAULT: blue)
cell_line_color	a color for tumor points (DEFAULT: orange)
use_gradient	a boolean, cell lines will appear with a gradient of colors with those with the cell_line_color being least similar to the tumors and those being similar to tumors will have a color closer to the tumor_color.
tumor_shape	an integer for an R plot PCH symbol (DEFAULT: 17)
cell_line_shape	an integer for an R plot PCH symbol (DEFAULT: 20)

Value

Nothing is returned

Author(s)

Rileen Sinha ([e-mail]), Augustin Luna ([e-mail])

See Also

run_comparison(), categorize_cell_lines()

run_comparison, categorize_cell_lines

Examples

# Generated using: tumorcomparer::run_comparison() 
comparison_result <- readRDS(system.file("test_output", "ov_comparison_result.rds", 
  package="tumorcomparer"))
  
plot_mds(comparison_result = comparison_result)

cannin/tumorcomparer documentation built on Feb. 7, 2023, 3:13 p.m.