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Ran through styler::style_dir() in the R and tests directories in preparation for #23.
This commit is contained in:
Waldir Leoncio 2021-11-10 14:02:35 +01:00
parent a9c7211465
commit fca9caa731
101 changed files with 3856 additions and 3869 deletions
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88
tests/testthat/test-greedyMix.R
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@ -2,73 +2,73 @@ context("Auxiliary functions to greedyMix")
# Defining the relative path to current inst -----------------------------------
if (interactive()) {
path_inst <- "../../inst/ext"
path_inst <- "../../inst/ext"
} else {
path_inst <- system.file("ext", "", package="rBAPS")
path_inst <- system.file("ext", "", package = "rBAPS")
}
# Reading datasets -------------------------------------------------------------
baps_diploid <- read.delim(
file = paste(path_inst, "BAPS_format_clustering_diploid.txt", sep="/"),
sep = " ",
header = FALSE
file = paste(path_inst, "BAPS_format_clustering_diploid.txt", sep = "/"),
sep = " ",
header = FALSE
)
test_that("handleData works as expected", {
data_obs <- handleData(baps_diploid)$newData
data_exp <- matrix(
c(
-9, 1, 2, 1, 1, 1, 2, 1, 2, 2, 1,
-9, 1, 1, 2, 2, 2, 1, 1, 1, 2, 1,
3, 2, 2, 3, 2, -9, 3, 1, 2, 1, 2,
2, 1, 2, 1, 2, -9, 1, 1, 1, 1, 2,
3, 1, 1, 1, 2, 1, 1, 2, -9, 1, 3,
3, 1, 2, 1, 1, 1, 2, 1, -9, 2, 3,
1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 4,
3, 2, 2, 3, 2, 2, 3, 1, 2, 1, 4,
2, 1, 2, 1, -9, 1, 1, 1, 1, 1, 5,
3, 1, 1, 1, -9, 1, 1, 2, 1, 1, 5
),
nrow = 10, byrow = TRUE
)
colnames(data_exp) <- colnames(data_obs)
expect_equal(data_obs, data_exp)
data_obs <- handleData(baps_diploid)$newData
data_exp <- matrix(
c(
-9, 1, 2, 1, 1, 1, 2, 1, 2, 2, 1,
-9, 1, 1, 2, 2, 2, 1, 1, 1, 2, 1,
3, 2, 2, 3, 2, -9, 3, 1, 2, 1, 2,
2, 1, 2, 1, 2, -9, 1, 1, 1, 1, 2,
3, 1, 1, 1, 2, 1, 1, 2, -9, 1, 3,
3, 1, 2, 1, 1, 1, 2, 1, -9, 2, 3,
1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 4,
3, 2, 2, 3, 2, 2, 3, 1, 2, 1, 4,
2, 1, 2, 1, -9, 1, 1, 1, 1, 1, 5,
3, 1, 1, 1, -9, 1, 1, 2, 1, 1, 5
),
nrow = 10, byrow = TRUE
)
colnames(data_exp) <- colnames(data_obs)
expect_equal(data_obs, data_exp)
})
context("Opening files on greedyMix")
df_fasta <- greedyMix(
data = file.path(path_inst, "FASTA_clustering_haploid.fasta"),
format = "FASTA"
data = file.path(path_inst, "FASTA_clustering_haploid.fasta"),
format = "FASTA"
)
df_vcf <- greedyMix(
data = file.path(path_inst, "vcf_example.vcf"),
format = "VCF",
verbose = FALSE
data = file.path(path_inst, "vcf_example.vcf"),
format = "VCF",
verbose = FALSE
)
df_bam <- greedyMix(
data = file.path(path_inst, "bam_example.bam"),
format = "BAM",
data = file.path(path_inst, "bam_example.bam"),
format = "BAM",
)
# TODO #19: add example reading Genpop
test_that("Files are imported correctly", {
expect_equal(dim(df_fasta), c(5, 99))
expect_equal(dim(df_vcf), c(variants = 2, fix_cols = 8, gt_cols = 3))
expect_error(
greedyMix(
data = paste(path_inst, "sam_example.sam", sep="/"),
format = "SAM",
)
)
expect_equal(length(df_bam[[1]]), 13)
expect_equal(dim(df_fasta), c(5, 99))
expect_equal(dim(df_vcf), c(variants = 2, fix_cols = 8, gt_cols = 3))
expect_error(
greedyMix(
data = paste(path_inst, "sam_example.sam", sep = "/"),
format = "SAM",
)
)
expect_equal(length(df_bam[[1]]), 13)
})
context("Linkage")
test_that("Linkages are properly calculated", {
Y <- c(0.5, 0.3, 0.6, 0.3, 0.3, 0.2, 0.3, 0.3, 0.3, 0.5)
expect_equal(
object = linkage(Y),
expected = matrix(c(2, 1, 7, 8, 4, 3, 5, 6, .2, .3, .3, .6), ncol=3)
)
Y <- c(0.5, 0.3, 0.6, 0.3, 0.3, 0.2, 0.3, 0.3, 0.3, 0.5)
expect_equal(
object = linkage(Y),
expected = matrix(c(2, 1, 7, 8, 4, 3, 5, 6, .2, .3, .3, .6), ncol = 3)
)
})