tests/testthat/testLoad.R

In DavidQuigley/HTDoseResponseCurve: Dose Response Curve Evaluation from Incucyte and Other High-Throughput Platforms

library(HTDoseResponseCurve)
context("Load data from files")

test_that("loading works", {
    pkg = "HTDoseResponseCurve"
    fn_data = system.file("extdata", "sample_data_96.xlsx", package = pkg)
    
    ds_raw = read_plates_from_Incucyte_export( fn_data, "plate_1", 
                                             number_of_wells=96)
    expect_equal( length(sort(unique((ds_raw$hours)))), 14)
    expect_equal( dim(ds_raw)[1], 112)
    expect_equal( dim(ds_raw)[2], 14)
    
    path_to_file= system.file("extdata", "sample_data_96_platemap.txt",
                              package=pkg )
    plate_map=read_platemap_from_Incucyte_XML( path_to_file )
    expect_equal( length(sort( unique( matrix( t(plate_map$treatment) ) ) )), 4)
    expect_equal( sum(plate_map$treatment=="Vehicle", na.rm=TRUE), 11 )
    expect_equal( plate_map$treatment[1,3], "drug_1")
    
    fn_map= system.file("extdata", "sample_data_96_platemap.xlsx",package=pkg)
    plate_map=read_platemap_from_excel( fn_map, number_of_wells=96)
        
    expect_equal( length(sort( unique( matrix( t(plate_map$treatment) ) ) )), 4)
    expect_equal( sum(plate_map$treatment=="Vehicle", na.rm = TRUE), 11 )
    expect_equal( plate_map$treatment[1,3], "drug_1")
    
    fn_data = system.file("extdata", "sample_data_synergy_platemap.xml", 
                          package = pkg)
    plate_map = read_platemap_from_Incucyte_XML(fn_data, 
                                                max_treatments_per_well = 2)
    
    fn_data = system.file("extdata", "sample_data_synergy_grid.txt", 
                          package = pkg)
    testd = read_dataset(fn_data, negative_control = 0)
    expect_equal( dim( testd )[1], 15 )
    expect_equal( sum(testd$is_negative_control, na.rm=TRUE), 7 )
    expect_equal( sum(testd$is_negative_control_2, na.rm=TRUE), 7 )
    fn_data = system.file("extdata", "sample_data_syn_malformed.txt", 
                          package = pkg)
    expect_error( read_dataset(fn_data, negative_control = 0), 
                  paste("if either concentrations_2 or treatments_2 is passed,",
                        "both parameters must be passed and must have the same",
                        "length"))
    # Test that if we try to load a synergy dataset using 1 treatment, it warns
    # in addition to throwing an error, so the user knows what the problem is
    fn_data = system.file("extdata", "sample_data_synergy_platemap.xml", 
                          package = pkg)
    suppressWarnings( expect_error( 
     read_platemap_from_Incucyte_XML(fn_data, max_treatments_per_well = 1 ), 
     "incorrect number of subscripts on matrix") )
} )