Skip to content

more work on unit tests #5

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ncborcherding merged 1 commit into from
Feb 28, 2026
Merged

more work on unit tests #5

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
251 changes: 251 additions & 0 deletions tests/testthat/test-clustering.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -668,3 +668,254 @@ test_that(".cluster_gliph2 generates save_cluster_list_df", {
expect_true("tag" %in% colnames(result$save_cluster_list_df))
}
})

# ---- .cluster_gliph2 verbose messaging ---------------------------------------

test_that(".cluster_gliph2 prints message when verbose is TRUE", {
d <- .make_cluster_data()

local_res <- data.frame(
motif = c("SL"),
start = c(1),
stop = c(2),
num_in_sample = c(3),
num_in_ref = c(10),
num_fold = c(5.0),
fisher.score = c(0.001),
members = paste(d$seqs[1:3], collapse = " "),
stringsAsFactors = FALSE
)

expect_message(
immGLIPH:::.cluster_gliph2(
local_res = local_res,
global_res = NULL,
sequences = d$sequences,
local_similarities = TRUE,
global_similarities = FALSE,
global_vgene = FALSE,
all_aa_interchangeable = TRUE,
structboundaries = TRUE,
boundary_size = 3,
motif_distance_cutoff = 10,
cluster_min_size = 1,
boost_local_significance = FALSE,
verbose = TRUE
),
"GLIPH2"
)
})

# ---- .cluster_gliph1 with patient.info = FALSE -------------------------------

test_that(".cluster_gliph1 works without patient info", {
seqs <- c("CASSLAPGATNEKLFF", "CASSLDRGEVFF", "CASSYLAGGRNTLYF")
sequences <- data.frame(
seq_ID = seq_along(seqs),
CDR3b = seqs,
TRBV = c("TRBV5-1", "TRBV6-2", "TRBV5-1"),
stringsAsFactors = FALSE
)

clone_network <- data.frame(
V1 = "CASSLAPGATNEKLFF",
V2 = "CASSLDRGEVFF",
type = "local",
stringsAsFactors = FALSE
)

result <- immGLIPH:::.cluster_gliph1(
clone_network = clone_network,
sequences = sequences,
not_in_global_ids = integer(0),
seqs = seqs,
vgene.info = TRUE,
patient.info = FALSE,
global_vgene = FALSE,
public_tcrs = TRUE,
cluster_min_size = 1,
verbose = FALSE
)

expect_type(result, "list")
expect_true(!is.null(result$cluster_properties))
})

# ---- .cluster_gliph2 with global_vgene TRUE includes TRBV in tag ------------

test_that(".cluster_gliph2 includes TRBV in tag when global_vgene is TRUE", {
d <- .make_cluster_data()

global_res <- data.frame(
cluster_tag = c("struct_%_13"),
cluster_size = c(3),
unique_CDR3b = c(3),
num_in_ref = c(5),
fisher.score = c(0.001),
aa_at_position = c("L"),
TRBV = c("TRBV5-1"),
CDR3b = paste(d$seqs[c(1, 3, 5)], collapse = " "),
stringsAsFactors = FALSE
)

result <- immGLIPH:::.cluster_gliph2(
local_res = NULL,
global_res = global_res,
sequences = d$sequences,
local_similarities = FALSE,
global_similarities = TRUE,
global_vgene = TRUE,
all_aa_interchangeable = TRUE,
structboundaries = TRUE,
boundary_size = 3,
motif_distance_cutoff = 1,
cluster_min_size = 1,
boost_local_significance = FALSE,
verbose = FALSE
)

if (!is.null(result$merged_clusters)) {
expect_true(any(grepl("TRBV", result$merged_clusters$tag)))
}
})

# ---- .cluster_gliph2 handles infinite OvE ------------------------------------

test_that(".cluster_gliph2 handles infinite OvE values", {
d <- .make_cluster_data()

local_res <- data.frame(
motif = c("SL"),
start = c(1),
stop = c(2),
num_in_sample = c(3),
num_in_ref = c(0),
num_fold = c(Inf),
fisher.score = c(0.001),
members = paste(d$seqs[1:3], collapse = " "),
stringsAsFactors = FALSE
)

result <- immGLIPH:::.cluster_gliph2(
local_res = local_res,
global_res = NULL,
sequences = d$sequences,
local_similarities = TRUE,
global_similarities = FALSE,
global_vgene = FALSE,
all_aa_interchangeable = TRUE,
structboundaries = TRUE,
boundary_size = 3,
motif_distance_cutoff = 10,
cluster_min_size = 1,
boost_local_significance = FALSE,
verbose = FALSE
)

expect_type(result, "list")
if (!is.null(result$merged_clusters)) {
# Infinite OvE should be replaced with 0
expect_true(all(is.finite(as.numeric(result$merged_clusters$OvE))))
}
})

# ---- .cluster_gliph1 duplicate cluster naming --------------------------------

test_that(".cluster_gliph1 handles duplicate cluster names with suffixes", {
# Create sequences where two separate components have the same first CDR3b
seqs <- c("CASSLAPGATNEKLFF", "CASSLDRGEVFF", "CASSLAPGATNEKLFF",
"CASSYLAGGRNTLYF")
sequences <- data.frame(
seq_ID = 1:4,
CDR3b = seqs,
TRBV = c("TRBV5-1", "TRBV6-2", "TRBV5-1", "TRBV7-2"),
patient = c("P1", "P1", "P2", "P2"),
stringsAsFactors = FALSE
)

clone_network <- data.frame(
V1 = c("CASSLAPGATNEKLFF", "CASSLAPGATNEKLFF"),
V2 = c("CASSLDRGEVFF", "CASSYLAGGRNTLYF"),
type = c("local", "local"),
stringsAsFactors = FALSE
)

result <- immGLIPH:::.cluster_gliph1(
clone_network = clone_network,
sequences = sequences,
not_in_global_ids = integer(0),
seqs = unique(seqs),
vgene.info = TRUE,
patient.info = TRUE,
global_vgene = FALSE,
public_tcrs = TRUE,
cluster_min_size = 1,
verbose = FALSE
)

expect_type(result, "list")
if (!is.null(result$cluster_properties)) {
# All tags should be unique
expect_equal(length(unique(result$cluster_properties$tag)),
nrow(result$cluster_properties))
}
})

# ---- .cluster_gliph2 motif_distance_cutoff restricts edges -------------------

test_that(".cluster_gliph2 motif_distance_cutoff = 0 eliminates positionally distant edges", {
d <- .make_cluster_data()

local_res <- data.frame(
motif = c("SL"),
start = c(1),
stop = c(2),
num_in_sample = c(3),
num_in_ref = c(10),
num_fold = c(5.0),
fisher.score = c(0.001),
members = paste(d$seqs[1:3], collapse = " "),
stringsAsFactors = FALSE
)

result_strict <- immGLIPH:::.cluster_gliph2(
local_res = local_res,
global_res = NULL,
sequences = d$sequences,
local_similarities = TRUE,
global_similarities = FALSE,
global_vgene = FALSE,
all_aa_interchangeable = TRUE,
structboundaries = TRUE,
boundary_size = 3,
motif_distance_cutoff = 0,
cluster_min_size = 1,
boost_local_significance = FALSE,
verbose = FALSE
)

result_lenient <- immGLIPH:::.cluster_gliph2(
local_res = local_res,
global_res = NULL,
sequences = d$sequences,
local_similarities = TRUE,
global_similarities = FALSE,
global_vgene = FALSE,
all_aa_interchangeable = TRUE,
structboundaries = TRUE,
boundary_size = 3,
motif_distance_cutoff = 100,
cluster_min_size = 1,
boost_local_significance = FALSE,
verbose = FALSE
)

# Strict cutoff should have fewer or equal edges
n_strict <- if (!is.null(result_strict$clone_network)) {
sum(result_strict$clone_network$type == "local", na.rm = TRUE)
} else 0
n_lenient <- if (!is.null(result_lenient$clone_network)) {
sum(result_lenient$clone_network$type == "local", na.rm = TRUE)
} else 0
expect_true(n_strict <= n_lenient)
})
Loading