Nothing
prefix <- tempdir()
# prefix <- "tests/testthat/" # nolint
# the writeLog-function needs the logfilename
logfilename <- paste0(prefix, "/log.txt")
# initialize our list for reactive values
rv <- list()
library(data.table)
test_that(
desc = "plotting_utility",
code = {
#"skip_on_cran()
rv$minmax <- FALSE
rv$sample_locus_name <- "Test"
rv$seed <- 1234
# create plotdir
plotdir <- paste0(prefix, "/plotdir/")
csvdir <- paste0(prefix, "/csvdir/")
on_start(plotdir = plotdir,
csvdir = csvdir,
logfilename = paste0(prefix, "/log.txt"),
parallel = FALSE)
# experimental data
exp_type_1 <- rBiasCorrection::example.data_experimental$dat
rv$fileimport_experimental <- clean_dt(exp_type_1,
"experimental",
1,
logfilename)[["dat"]]
# calibration data
cal_type_1 <- rBiasCorrection::example.data_calibration$dat
cal_type_1 <- clean_dt(cal_type_1, "calibration", 1, logfilename)
rv$fileimport_calibration <- cal_type_1[["dat"]]
rv$vec_cal <- cal_type_1[["vec_cal"]]
# reconstruct parts from app_plottingUtility.R
regression_results <- regression_utility(
data = rv$fileimport_calibration,
samplelocusname = "Testlocus",
locus_id = NULL,
rv = rv,
mode = NULL,
logfilename = logfilename,
minmax = rv$minmax,
seed = rv$seed
)
plotlist_reg <- regression_results[["plot_list"]]
rv$result_list <- regression_results[["result_list"]]
# create calibration plots
virtual_list <- plotting_utility(
data = rv$fileimport_calibration,
plotlist_reg = plotlist_reg,
type = 1,
samplelocusname = rv$sample_locus_name,
locus_id = NULL,
rv = rv,
mode = NULL,
plotdir = plotdir,
logfilename = logfilename,
minmax = rv$minmax,
plot_height = 5,
plot_width = 7.5,
plot_textsize = 1
)
expect_type(virtual_list, "list")
expect_length(list.files(plotdir), 10)
# cleanup
expect_silent(clean_up(plotdir = plotdir,
csvdir = csvdir))
})
test_that(
desc = "createbarerrorplots",
code = {
#"skip_on_cran()
rv$minmax <- FALSE
rv$sample_locus_name <- "Test"
rv$seed <- 1234
# create plotdir
plotdir <- paste0(prefix, "/plotdir/")
csvdir <- paste0(prefix, "/csvdir/")
on_start(plotdir = plotdir,
csvdir = csvdir,
logfilename = paste0(prefix, "/log.txt"),
parallel = FALSE)
# experimental data
exp_type_1 <- rBiasCorrection::example.data_experimental$dat
rv$fileimport_experimental <- clean_dt(exp_type_1,
"experimental",
1,
logfilename)[["dat"]]
# calibration data
cal_type_1 <- rBiasCorrection::example.data_calibration$dat
cal_type_1 <- clean_dt(cal_type_1, "calibration", 1, logfilename)
rv$fileimport_calibration <- cal_type_1[["dat"]]
rv$vec_cal <- cal_type_1[["vec_cal"]]
# reconstruct parts from app_plottingUtility.R
regression_results <- regression_utility(
data = rv$fileimport_calibration,
samplelocusname = "Testlocus",
locus_id = NULL,
rv = rv,
mode = NULL,
logfilename = logfilename,
minmax = rv$minmax,
seed = rv$seed
)
rv$result_list <- regression_results[["result_list"]]
# get regression statistics
rv$reg_stats <- statistics_list(
rv$result_list,
minmax = rv$minmax
)
# select the better model based on the sum of squared errrors ("SSE")
rv$choices_list <- better_model(
statstable_pre = rv$reg_stats,
selection_method = "SSE"
)
# correct calibration data (to show corrected calibration curves)
solved_eq_h <- solving_equations(datatable = rv$fileimport_calibration,
regmethod = rv$choices_list,
type = 1,
rv = rv,
mode = "corrected",
logfilename = logfilename,
minmax = rv$minmax)
rv$fileimport_cal_corrected_h <- solved_eq_h$results
colnames(rv$fileimport_cal_corrected_h) <- colnames(
rv$fileimport_calibration
)
# calculate new calibration curves from corrected calibration data
regression_results <- regression_utility(
data = rv$fileimport_cal_corrected_h,
samplelocusname = rv$sample_locus_name,
rv = rv,
mode = "corrected",
logfilename = logfilename,
minmax = rv$minmax,
seed = rv$seed
)
rv$result_list_hyperbolic <- regression_results$result_list
# save regression statistics to reactive value
rv$reg_stats_corrected_h <- statistics_list(
resultlist = rv$result_list_hyperbolic,
minmax = rv$minmax
)
virtual_list <- createbarerrorplots(
statstable_pre = rv$reg_stats,
statstable_post = rv$reg_stats_corrected_h,
rv = rv,
type = 1,
locus_id = NULL,
plotdir = plotdir,
logfilename = logfilename,
mode = "corrected_h",
plot_height = 5,
plot_width = 7.5,
plot_textsize = 1
)
expect_type(virtual_list, "list")
expect_length(list.files(plotdir), 10)
# cleanup
expect_silent(clean_up(plotdir = plotdir,
csvdir = csvdir))
})
test_that(
desc = "create_exampleplot",
code = {
#"skip_on_cran()
rv$minmax <- FALSE
rv$sample_locus_name <- "Test"
rv$seed <- 1234
# create plotdir
plotdir <- paste0(prefix, "/plotdir/")
csvdir <- paste0(prefix, "/csvdir/")
on_start(plotdir = plotdir,
csvdir = csvdir,
logfilename = paste0(prefix, "/log.txt"),
parallel = FALSE)
gdat <- rBiasCorrection::example._plot.df_agg
coef_h <- rBiasCorrection::example._plot_coef_h
coef_c <- rBiasCorrection::example._plot_coef_c
virtual_list <- create_exampleplot(
data = gdat,
coef_hyper = coef_h,
coef_cubic = coef_c,
plot_height = 5,
plot_width = 7.5,
plot_textsize = 1,
filename = paste0(plotdir, "/exampleplot.png")
)
expect_type(virtual_list, "character")
expect_length(list.files(plotdir), 1)
# cleanup
expect_silent(clean_up(plotdir = plotdir,
csvdir = csvdir))
expect_true(file.remove(paste0(prefix, "/log.txt")))
})
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