tests/testthat/test-bulk_methods_SummarizedExperiment.R
In stemangiola/tidyBulk: Brings transcriptomics to the tidyverse
context('Bulk methods SummarizedExperiment')
data("se_mini")
data("breast_tcga_mini_SE")
input_df = se_mini |> tidybulk() |> as_tibble() |> setNames( c( "b","a", "c", "Cell type", "time" , "condition", "days", "dead", "entrez"))
input_df_breast = setNames( breast_tcga_mini_SE |> tidybulk() |> as_tibble(), c( "b", "a","c", "c norm", "call" ))
test_that("tidybulk SummarizedExperiment conversion",{
res = tidybulk(tidybulk::se)
expect_equal( class(res)[1], "tidybulk" )
expect_equal( nrow(res), 800 )
expect_equal( ncol(res), 13 )
res = res |> tidybulk:::tidybulk_to_SummarizedExperiment()
expect_equal( class(res)[1], "SummarizedExperiment" )
expect_equal( nrow(res), 100 )
expect_equal( ncol(res), 8 )
})
test_that("tidybulk SummarizedExperiment normalisation manual",{
res = tidybulk(tidybulk:::tidybulk_to_SummarizedExperiment(scale_abundance(tidybulk(se) |> identify_abundant())))
res2 = tidybulk(se) |> identify_abundant() |> scale_abundance()
res |> distinct(.sample, multiplier) |> pull(multiplier)
res2 |> distinct(.sample, multiplier) |> pull(multiplier)
expect_equal(
res |> distinct(.sample, multiplier) |> pull(multiplier),
res2 |> distinct(.sample, multiplier) |> pull(multiplier) |> as.numeric(),
tolerance=1e-3
)
expect_equal( nrow(res), 800 )
expect_equal( ncol(res), 17 )
res = rlang::quo_name(attr(res, "internals")$tt_columns[[4]])
expect_equal( res, "counts_scaled" )
})
test_that("tidybulk SummarizedExperiment normalisation",{
res = se |> identify_abundant() |> scale_abundance()
expect_equal(
names(SummarizedExperiment::assays(res)),
c("counts" ,"counts_scaled")
)
})
test_that("quantile normalisation",{
res = se_mini |> quantile_normalise_abundance()
res_tibble =
input_df |>
quantile_normalise_abundance(
.sample = a,
.transcript = b,
.abundance = c,
action = "get"
)
SummarizedExperiment::assay(res, "count_scaled")["ABCB9","SRR1740035"] |>
expect_equal(
res_tibble |>
filter(a=="SRR1740035" & b=="ABCB9") |>
dplyr::pull(c_scaled)
)
# preprocessCore
res = se_mini |> quantile_normalise_abundance(method = "preprocesscore_normalize_quantiles_use_target")
res_tibble =
input_df |>
quantile_normalise_abundance(
.sample = a,
.transcript = b,
.abundance = c,
method = "preprocesscore_normalize_quantiles_use_target",
action = "get"
)
SummarizedExperiment::assay(res, "count_scaled")["ABCB9","SRR1740035"] |>
expect_equal(
res_tibble |>
filter(a=="SRR1740035" & b=="ABCB9") |>
dplyr::pull(c_scaled)
)
target_distribution =
se_mini |>
assay( "count") |>
as.matrix() |>
preprocessCore::normalize.quantiles.determine.target()
se_mini |>
quantile_normalise_abundance(
method = "preprocesscore_normalize_quantiles_use_target",
target_distribution = target_distribution
) |>
expect_no_error()
})
test_that("tidybulk SummarizedExperiment normalisation subset",{
res = se |> identify_abundant() |> scale_abundance(
.subset_for_scaling = .abundant & grepl("^E", .feature)
)
expect_equal(
unique(SummarizedExperiment::colData(res)$multiplier),
c(1.3648110, 1.5756592, 1.1651309, 2.1282288, 1.2110911, 0.9574359, 1.4434610, 1.4897840),
tolerance=1e-3
)
})
test_that("tidybulk SummarizedExperiment clustering",{
res = cluster_elements(se, method="kmeans", centers = 2)
expect_equal(
tail(names(SummarizedExperiment::colData(res)), 1),
"cluster_kmeans"
)
expect_equal(
levels(SummarizedExperiment::colData(res)$cluster_kmeans),
c("1", "2")
)
})
test_that("tidybulk SummarizedExperiment clustering",{
res = se |> identify_abundant() |> reduce_dimensions(method="PCA")
expect_equal(
tail(names(SummarizedExperiment::colData(res)), 1),
"PC2"
)
})
test_that("Get rotated dimensions - SummarizedExperiment",{
res.pca =
reduce_dimensions(se |> identify_abundant(), method="PCA" )
res =
rotate_dimensions(
res.pca,
dimension_1_column = PC1,
dimension_2_column = PC2,
rotation_degrees = 45
)
expect_equal(
tail(names(SummarizedExperiment::colData(res)), 1),
"PC2_rotated_45"
)
})
test_that("Drop redundant correlated - SummarizedExperiment",{
res =
remove_redundancy(
se,
method = "correlation", correlation_threshold = 0.99 )
expect_equal(
nrow(res),
100
)
})
test_that("Get adjusted counts - SummarizedExperiment",{
cm = se_mini
cm$batch = 0
cm$batch[colnames(cm) %in% c("SRR1740035", "SRR1740043")] = 1
res =
cm |>
identify_abundant() |>
adjust_abundance(
~ condition + batch,
method = "combat"
)
expect_equal(nrow(res), 527 )
expect_equal( names(SummarizedExperiment::assays(res)), c("count" ,"count_adjusted") )
})
test_that("Get adjusted counts multiple factors - SummarizedExperiment",{
cm = se_mini
cm$batch = 0
cm$batch[colnames(cm) %in% c("SRR1740035", "SRR1740043")] = 1
cm =
cm |>
identify_abundant() |>
scale_abundance()
cm@assays@data$count_scaled = apply(cm@assays@data$count_scaled, 2, as.integer)
res =
cm |>
adjust_abundance(.factor_unwanted = c(batch),
.factor_of_interest = time,
.abundance = count_scaled,
method = "combat_seq",
shrink.disp = TRUE,
shrink = TRUE,
gene.subset.n = 100
)
expect_equal(nrow(res), 527 )
expect_equal( names(SummarizedExperiment::assays(res)), c("count" , "count_scaled", "count_scaled_adjusted") )
})
test_that("Aggregate duplicated transcript - SummarizedExperiment",{
se = tidybulk::se
SummarizedExperiment::rowData(se)$bla =
rownames(se) |> purrr::map_chr(~ {
if(.x %in% c("LRG_239", "LRG_405")) "BLAAA"
else .x
})
rowData(se)$bla = if_else(rowData(se)$bla %in% c("LRG_239", "LRG_405"), "BLAAA", rowData(se)$bla )
res = aggregate_duplicates(se, .transcript = bla )
expect_equal(
as.data.frame(rowRanges(se["ENSG00000272397","SRR1039508"])) |>
mutate_if(is.factor, as.character),
as.data.frame(rowRanges(res["ENSG00000272397","SRR1039508"]))|>
mutate_if(is.factor, as.character),
)
expect_equal( dim(res), c( 99, 8 ) )
})
test_that("Add cell type proportions - SummarizedExperiment",{
res = deconvolve_cellularity(se_mini, cores=1 )
expect_equal(
as.numeric(as.data.frame(res@colData[1, 6:9])),
c( 0.619662 , 0.25256 , 0 , 0),
tolerance=1e-3
)
})
test_that("differential trancript abundance - SummarizedExperiment",{
res = test_differential_abundance(
se_mini |>
identify_abundant(factor_of_interest = condition),
~ condition
)
w = match( c("CLEC7A" , "FAM198B", "FCN1" , "HK3" ), rownames(res) )
# Quasi likelihood
res_tibble = test_differential_abundance(
input_df |> identify_abundant(a, b, c, factor_of_interest = condition),
~ condition ,
a, b, c
)
expect_equal(
res@elementMetadata[w,]$logFC,
c(-11.58385, -13.53406, -12.58204, -12.19271),
tolerance=1e-3
)
expect_equal(
res@elementMetadata[w,]$logFC,
res_tibble |>
pivot_transcript(b) |>
filter(b %in% rownames(res)[w]) |>
dplyr::arrange(b) |>
dplyr::pull(logFC),
tolerance=1e-3
)
# Likelihood ratio
res2 = test_differential_abundance(
se_mini |>
identify_abundant(factor_of_interest = condition),
~ condition, method = "edgeR_likelihood_ratio" )
res2_tibble = test_differential_abundance(
input_df |> identify_abundant(a, b, c, factor_of_interest = condition),
~ condition ,
a, b, c, method = "edgeR_likelihood_ratio"
)
expect_equal(
res2@elementMetadata[w,]$logFC,
c(-11.57989, -13.53476, -12.57969, -12.19303),
tolerance=1e-3
)
expect_equal(
res2@elementMetadata[w,]$logFC,
res2_tibble |>
pivot_transcript(b) |>
filter(b %in% rownames(res)[w]) |>
dplyr::arrange(b) |>
dplyr::pull(logFC),
tolerance=1e-3
)
# Treat
se_mini |>
identify_abundant(factor_of_interest = condition) |>
test_differential_abundance(
~ condition,
scaling_method = "TMM",
method = "edgeR_likelihood_ratio",
test_above_log2_fold_change = 1,
action="only"
) |> SummarizedExperiment::rowData() |>
as_tibble() |>
filter(FDR<0.05) |>
nrow() |>
expect_equal(171)
})
test_that("differential trancript abundance - SummarizedExperiment - alternative .abundance",{
library(SummarizedExperiment)
assays(se_mini) = list(counts = assay(se_mini), bla = assay(se_mini))
res = se_mini |>
identify_abundant(factor_of_interest = condition) |>
test_differential_abundance( ~ condition , .abundance = bla)
w = match( c("CLEC7A" , "FAM198B", "FCN1" , "HK3" ), rownames(res) )
# Quasi likelihood
res_tibble = test_differential_abundance(
input_df |> identify_abundant(a, b, c, factor_of_interest = condition),
~ condition ,
a, b, c
)
expect_equal(
res@elementMetadata[w,]$logFC,
c(-11.58385, -13.53406, -12.58204, -12.19271),
tolerance=1e-3
)
expect_equal(
res@elementMetadata[w,]$logFC,
res_tibble |>
pivot_transcript(b) |>
filter(b %in% rownames(res)[w]) |>
dplyr::arrange(b) |>
dplyr::pull(logFC),
tolerance=1e-3
)
# Likelihood ratio
res2 = test_differential_abundance(
se_mini |>
identify_abundant(factor_of_interest = condition),
~ condition, .abundance = bla, method = "edgeR_likelihood_ratio" )
res2_tibble = test_differential_abundance(
input_df |> identify_abundant(a, b, c, factor_of_interest = condition),
~ condition ,
a, b, c, method = "edgeR_likelihood_ratio"
)
expect_equal(
res2@elementMetadata[w,]$logFC,
c(-11.57989, -13.53476, -12.57969, -12.19303),
tolerance=1e-3
)
expect_equal(
res2@elementMetadata[w,]$logFC,
res2_tibble |>
pivot_transcript(b) |>
filter(b %in% rownames(res)[w]) |>
dplyr::arrange(b) |>
dplyr::pull(logFC),
tolerance=1e-3
)
# Treat
se_mini |>
identify_abundant( factor_of_interest = condition) |>
test_differential_abundance(
~ condition, .abundance = bla,
scaling_method = "TMM",
method = "edgeR_likelihood_ratio",
test_above_log2_fold_change = 1,
action="only"
) |> SummarizedExperiment::rowData() |>
as_tibble() |>
filter(FDR<0.05) |>
nrow() |>
expect_equal(171)
})
test_that("DE interaction effects", {
# Att interaction factor
col_data = colData(breast_tcga_mini_SE)
set.seed(42)
col_data$interaction_term = sample(c(0,1), size = nrow(col_data), replace = TRUE)
colData(breast_tcga_mini_SE) = col_data
breast_tcga_mini_SE |>
identify_abundant(factor_of_interest = Call) |>
test_differential_abundance(
~ Call * interaction_term,
contrasts = "CallHer2___interaction_term",
method="edgeR_quasi_likelihood"
) |>
expect_no_error()
})
test_that("Voom with treat method",{
se_mini |>
identify_abundant(factor_of_interest = condition) |>
test_differential_abundance(
~ condition,
method = "limma_voom",
test_above_log2_fold_change = 1,
action="only"
) |> SummarizedExperiment::rowData() |>
as_tibble() |>
filter(adj.P.Val<0.05) |>
nrow() |>
expect_equal(97)
# with multiple contrasts
res <-
se_mini |>
identify_abundant( factor_of_interest = Cell.type) |>
test_differential_abundance(
~ 0 + Cell.type,
.contrasts = c("Cell.typeb_cell-Cell.typemonocyte", "Cell.typeb_cell-Cell.typet_cell"),
method = "limma_voom",
test_above_log2_fold_change = 1,
action="only"
) |> SummarizedExperiment::rowData() |>
as_tibble()
res |>
filter(adj.P.Val___Cell.typeb_cell.Cell.typemonocyte < 0.05) |>
nrow() |>
expect_equal(294)
res |>
filter(adj.P.Val___Cell.typeb_cell.Cell.typet_cell < 0.05) |>
nrow() |>
expect_equal(246)
})
test_that("differential trancript abundance - random effects SE",{
set.seed(42)
res =
se_mini[1:10,] |>
identify_abundant(factor_of_interest = condition) |>
#mutate(time = time |> stringr::str_replace_all(" ", "_")) |>
test_differential_abundance(
~ condition + (1 + condition | time),
method = "glmmseq_lme4",
cores = 1
)
rowData(res)[,"P_condition_adjusted"] |>
head(4) |>
expect_equal(
c(0.1578695, 0.1221392, 0.1221392, 0.2262688),
tolerance=1e-2
)
# Custom dispersion
se_mini =
se_mini |>
identify_abundant(factor_of_interest = condition)
rowData(se_mini)$disp_ = rep(2,nrow(se_mini))
res =
se_mini[1:10,] |>
#mutate(time = time |> stringr::str_replace_all(" ", "_")) |>
test_differential_abundance(
~ condition + (1 + condition | time),
method = "glmmseq_lme4",
.dispersion = disp_,
cores = 1
)
rowData(res)[,"P_condition_adjusted"] |>
head(4) |>
expect_equal(
c(0.2633982, 0.2633982, 0.2633982, 0.5028348),
tolerance=1e-2
)
})
test_that("filter abundant - SummarizedExperiment",{
res = keep_abundant( se )
expect_equal( nrow(res), 23 )
})
test_that("filter variable - no object",{
res = keep_variable(se, top = 5 )
expect_equal( nrow(res),5 )
res =
keep_variable(
se_mini,
top = 5
)
expect_equal( nrow(res),5 )
expect_equivalent(
sort(rownames(res)),
c("FCN1", "IGHD", "IGHM", "IGKC", "TCL1A")
)
})
test_that("impute missing",{
res =
input_df |>
dplyr::slice(-1) |>
tidybulk:::tidybulk_to_SummarizedExperiment(a, b, c) |>
impute_missing_abundance( ~ condition )
list_SE = SummarizedExperiment::assays(res) |> as.list()
list_SE[[1]]["TNFRSF4", "SRR1740034"] |>
expect_equal(6)
expect_equal( nrow(res)*ncol(res), nrow(input_df) )
})
test_that("differential composition",{
# Cibersort
se_mini |>
test_differential_cellularity(. ~ condition , cores = 1 ) |>
pull(`estimate_(Intercept)`) |>
magrittr::extract2(1) |>
as.integer() |>
expect_equal( -2, tollerance =1e-3)
# llsr
se_mini |>
test_differential_cellularity(
. ~ condition,
method="llsr"
) |>
pull(`estimate_(Intercept)`) |>
magrittr::extract2(1) |>
as.integer() |>
expect_equal( -2, tollerance =1e-3)
# Survival analyses
input_df |>
dplyr::select(a, b, c) |>
nest(data = -a) |>
mutate(
days = c(1, 10, 500, 1000, 2000),
dead = c(1, 1, 1, 0, 1)
) |>
unnest(data) |>
tidybulk:::tidybulk_to_SummarizedExperiment(a, b, c) |>
test_differential_cellularity(
survival::Surv(days, dead) ~ .,
cores = 1
) |>
pull(estimate) |>
magrittr::extract2(1) |>
expect_equal(26.2662279, tolerance = 30)
# round() %in% c(
# 26, # 97 is the github action MacOS that has different value
# 26, # 112 is the github action UBUNTU that has different value
# 26 # 93 is the github action Windows that has different value
# ) |>
# expect_true()
})
test_that("test_stratification_cellularity",{
# Cibersort
input_df |>
select(a, b, c) |>
nest(data = -a) |>
mutate(
days = c(1, 10, 500, 1000, 2000),
dead = c(1, 1, 1, 0, 1)
) |>
unnest(data) |>
tidybulk:::tidybulk_to_SummarizedExperiment(a, b, c) |>
test_stratification_cellularity(
survival::Surv(days, dead) ~ .,
cores = 1
) |>
pull(.low_cellularity_expected) |>
magrittr::extract2(1) |>
expect_equal(3.35, tolerance =1e-1)
# llsr
input_df |>
select(a, b, c) |>
nest(data = -a) |>
mutate(
days = c(1, 10, 500, 1000, 2000),
dead = c(1, 1, 1, 0, 1)
) |>
unnest(data) |>
test_stratification_cellularity(
survival::Surv(days, dead) ~ .,
.sample = a,
.transcript = b,
.abundance = c,
method = "llsr"
) |>
pull(.low_cellularity_expected) |>
magrittr::extract2(1) |>
expect_equal(3.35, tolerance =1e-1)
})
# test_that("Get gene enrichment - no object",{
#
# if (find.package("EGSEA", quiet = TRUE) |> length |> equals(0)) {
# message("Installing EGSEA needed for differential transcript abundance analyses")
# if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager", repos = "https://cloud.r-project.org")
# BiocManager::install("EGSEA")
# }
#
# library(EGSEA)
#
# res =
# aggregate_duplicates(
# dplyr::rename(symbol_to_entrez(
# #dplyr::filter(input_df, grepl("^B", b)),
# input_df,
# .transcript = b, .sample = a), d = entrez
# ),
# .transcript = d,
# .sample = a,
# .abundance = c
# ) |> identify_abundant(a, b, c, factor_of_interest = condition) |>
# tidybulk:::tidybulk_to_SummarizedExperiment(a, b, c) |>
# test_gene_enrichment(
# ~ condition,
# .entrez = d,
# species="human"
# )
#
# expect_equal(
# res$pathway[1:4],
# c("GNF2_HCK" , "GSE10325_LUPUS_BCELL_VS_LUPUS_MYELOID_DN" ,"Amino sugar and nucleotide sugar metabolism", "Phagosome" )
# )
#
# expect_equal(
# ncol(res),
# 20
# )
#
# })
test_that("pivot",{
expect_equal( ncol(pivot_sample(se_mini) ), 6)
expect_equal( ncol(pivot_transcript(se_mini) ), 2)
})
test_that("gene over representation",{
df_entrez = aggregate_duplicates(input_df, aggregation_function = sum, .sample = a, .transcript = entrez, .abundance = c)
df_entrez = mutate(df_entrez, do_test = b %in% c("TNFRSF4", "PLCH2", "PADI4", "PAX7"))
res =
df_entrez |>
tidybulk:::tidybulk_to_SummarizedExperiment(a, b, c) |>
test_gene_overrepresentation(
.entrez = entrez,
.do_test = do_test,
species="Homo sapiens"
)
expect_equal( ncol(res), 13 )
})
test_that("Only reduced dimensions MDS - no object",{
res =
breast_tcga_mini_SE |>
reduce_dimensions(method = "MDS")
expect_equal(
res$`Dim1`[1:4],
c(-0.2723808836, -0.1105770207, -0.3034092668, -0.0064569358),
tolerance=10
)
expect_equal(
ncol(SummarizedExperiment::colData(res)),
3
)
expect_equal( class(attr(res, "internals")$MDS[[1]])[1], "MDS" )
})
test_that("Only reduced dimensions PCA - no object",{
res =
breast_tcga_mini_SE |>
reduce_dimensions( method = "PCA" )
expect_equal(
res$`PC1`[1:4],
c(-8.5145575 , 4.2451190 , -6.8991306 , -6.0787597 ),
tolerance=10
)
expect_equal(
ncol(SummarizedExperiment::colData(res)),
3
)
expect_equal( class(attr(res, "internals")$PCA[[1]])[1], "numeric" )
})
test_that("Only reduced dimensions tSNE - no object",{
res =
breast_tcga_mini_SE |>
reduce_dimensions( method = "tSNE" )
expect_equal(
res$`tSNE1`[1:4],
c(-2.4677708, -0.3447403, -5.8059667, 1.9685007 ),
tolerance=10
)
expect_equal(
ncol(SummarizedExperiment::colData(res)),
3
)
expect_equal( class(attr(res, "internals")$tSNE[[1]])[1], "integer" )
})
test_that("Only reduced dimensions UMAP - no object",{
res =
breast_tcga_mini_SE |>
reduce_dimensions( method = "UMAP" )
expect_equal(
res$`UMAP1`[1:4],
c(-1.9784263, -0.8536380, -0.6537955, -1.8840860 ),
tolerance=10
)
expect_equal(
ncol(SummarizedExperiment::colData(res)),
3
)
expect_equal( class(attr(res, "internals")$UMAP[[1]])[1], "numeric" )
})
test_that("resolve_complete_confounders_of_non_interest",{
#library(tidySummarizedExperiment)
library(SummarizedExperiment)
# Sample annotations
sample_annotations <- data.frame(
sample_id = paste0("Sample", seq(1, 9)),
factor_of_interest = c(rep("treated", 4), rep("untreated", 5)),
A = c("a1", "a2", "a1", "a2", "a1", "a2", "a1", "a2", "a3"),
B = c("b1", "b1", "b2", "b1", "b1", "b1", "b2", "b1", "b3"),
C = c("c1", "c1", "c1", "c1", "c1", "c1", "c1", "c1", "c3"),
stringsAsFactors = FALSE
)
# Simulated assay data (e.g., gene expression data)
# Let's assume we have 100 genes (rows) and 9 samples (columns)
assay_data <- matrix(rnorm(100 * 9), nrow = 100, ncol = 9)
# Row data (e.g., gene annotations)
# For simplicity, we'll just use a sequence of gene IDs
row_data <- data.frame(gene_id = paste0("Gene", seq_len(100)))
# Create SummarizedExperiment object
se <- SummarizedExperiment(assays = list(counts = assay_data),
rowData = row_data,
colData = DataFrame(sample_annotations))
expected_tibble =
tibble(
.sample = c("1", "5", "2", "4", "6", "8", "9", "3", "7"),
A = c("a1", "a1", "a2", "a2", "a2", "a2", "a3", "a1", "a1"),
B = c("b1", "b1", "b1", "b1", "b1", "b1", "b1", "b2", "b2"),
C = rep("c1", 9)
) |> arrange(.sample)
se |>
resolve_complete_confounders_of_non_interest(A, B, C) |>
colData() |>
_[, c("A", "B", "C")] |>
as_tibble(rownames = ".sample") |>
expect_identical(expected_tibble )
})
stemangiola/tidyBulk documentation built on Oct. 22, 2024, 5:19 a.m.
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context('Bulk methods SummarizedExperiment')
data("se_mini")
data("breast_tcga_mini_SE")
input_df = se_mini |> tidybulk() |> as_tibble() |> setNames( c( "b","a", "c", "Cell type", "time" , "condition", "days", "dead", "entrez"))
input_df_breast = setNames( breast_tcga_mini_SE |> tidybulk() |> as_tibble(), c( "b", "a","c", "c norm", "call" ))
test_that("tidybulk SummarizedExperiment conversion",{
res = tidybulk(tidybulk::se)
expect_equal( class(res)[1], "tidybulk" )
expect_equal( nrow(res), 800 )
expect_equal( ncol(res), 13 )
res = res |> tidybulk:::tidybulk_to_SummarizedExperiment()
expect_equal( class(res)[1], "SummarizedExperiment" )
expect_equal( nrow(res), 100 )
expect_equal( ncol(res), 8 )
})
test_that("tidybulk SummarizedExperiment normalisation manual",{
res = tidybulk(tidybulk:::tidybulk_to_SummarizedExperiment(scale_abundance(tidybulk(se) |> identify_abundant())))
res2 = tidybulk(se) |> identify_abundant() |> scale_abundance()
res |> distinct(.sample, multiplier) |> pull(multiplier)
res2 |> distinct(.sample, multiplier) |> pull(multiplier)
expect_equal(
res |> distinct(.sample, multiplier) |> pull(multiplier),
res2 |> distinct(.sample, multiplier) |> pull(multiplier) |> as.numeric(),
tolerance=1e-3
)
expect_equal( nrow(res), 800 )
expect_equal( ncol(res), 17 )
res = rlang::quo_name(attr(res, "internals")$tt_columns[[4]])
expect_equal( res, "counts_scaled" )
})
test_that("tidybulk SummarizedExperiment normalisation",{
res = se |> identify_abundant() |> scale_abundance()
expect_equal(
names(SummarizedExperiment::assays(res)),
c("counts" ,"counts_scaled")
)
})
test_that("quantile normalisation",{
res = se_mini |> quantile_normalise_abundance()
res_tibble =
input_df |>
quantile_normalise_abundance(
.sample = a,
.transcript = b,
.abundance = c,
action = "get"
)
SummarizedExperiment::assay(res, "count_scaled")["ABCB9","SRR1740035"] |>
expect_equal(
res_tibble |>
filter(a=="SRR1740035" & b=="ABCB9") |>
dplyr::pull(c_scaled)
)
# preprocessCore
res = se_mini |> quantile_normalise_abundance(method = "preprocesscore_normalize_quantiles_use_target")
res_tibble =
input_df |>
quantile_normalise_abundance(
.sample = a,
.transcript = b,
.abundance = c,
method = "preprocesscore_normalize_quantiles_use_target",
action = "get"
)
SummarizedExperiment::assay(res, "count_scaled")["ABCB9","SRR1740035"] |>
expect_equal(
res_tibble |>
filter(a=="SRR1740035" & b=="ABCB9") |>
dplyr::pull(c_scaled)
)
target_distribution =
se_mini |>
assay( "count") |>
as.matrix() |>
preprocessCore::normalize.quantiles.determine.target()
se_mini |>
quantile_normalise_abundance(
method = "preprocesscore_normalize_quantiles_use_target",
target_distribution = target_distribution
) |>
expect_no_error()
})
test_that("tidybulk SummarizedExperiment normalisation subset",{
res = se |> identify_abundant() |> scale_abundance(
.subset_for_scaling = .abundant & grepl("^E", .feature)
)
expect_equal(
unique(SummarizedExperiment::colData(res)$multiplier),
c(1.3648110, 1.5756592, 1.1651309, 2.1282288, 1.2110911, 0.9574359, 1.4434610, 1.4897840),
tolerance=1e-3
)
})
test_that("tidybulk SummarizedExperiment clustering",{
res = cluster_elements(se, method="kmeans", centers = 2)
expect_equal(
tail(names(SummarizedExperiment::colData(res)), 1),
"cluster_kmeans"
)
expect_equal(
levels(SummarizedExperiment::colData(res)$cluster_kmeans),
c("1", "2")
)
})
test_that("tidybulk SummarizedExperiment clustering",{
res = se |> identify_abundant() |> reduce_dimensions(method="PCA")
expect_equal(
tail(names(SummarizedExperiment::colData(res)), 1),
"PC2"
)
})
test_that("Get rotated dimensions - SummarizedExperiment",{
res.pca =
reduce_dimensions(se |> identify_abundant(), method="PCA" )
res =
rotate_dimensions(
res.pca,
dimension_1_column = PC1,
dimension_2_column = PC2,
rotation_degrees = 45
)
expect_equal(
tail(names(SummarizedExperiment::colData(res)), 1),
"PC2_rotated_45"
)
})
test_that("Drop redundant correlated - SummarizedExperiment",{
res =
remove_redundancy(
se,
method = "correlation", correlation_threshold = 0.99 )
expect_equal(
nrow(res),
100
)
})
test_that("Get adjusted counts - SummarizedExperiment",{
cm = se_mini
cm$batch = 0
cm$batch[colnames(cm) %in% c("SRR1740035", "SRR1740043")] = 1
res =
cm |>
identify_abundant() |>
adjust_abundance(
~ condition + batch,
method = "combat"
)
expect_equal(nrow(res), 527 )
expect_equal( names(SummarizedExperiment::assays(res)), c("count" ,"count_adjusted") )
})
test_that("Get adjusted counts multiple factors - SummarizedExperiment",{
cm = se_mini
cm$batch = 0
cm$batch[colnames(cm) %in% c("SRR1740035", "SRR1740043")] = 1
cm =
cm |>
identify_abundant() |>
scale_abundance()
cm@assays@data$count_scaled = apply(cm@assays@data$count_scaled, 2, as.integer)
res =
cm |>
adjust_abundance(.factor_unwanted = c(batch),
.factor_of_interest = time,
.abundance = count_scaled,
method = "combat_seq",
shrink.disp = TRUE,
shrink = TRUE,
gene.subset.n = 100
)
expect_equal(nrow(res), 527 )
expect_equal( names(SummarizedExperiment::assays(res)), c("count" , "count_scaled", "count_scaled_adjusted") )
})
test_that("Aggregate duplicated transcript - SummarizedExperiment",{
se = tidybulk::se
SummarizedExperiment::rowData(se)$bla =
rownames(se) |> purrr::map_chr(~ {
if(.x %in% c("LRG_239", "LRG_405")) "BLAAA"
else .x
})
rowData(se)$bla = if_else(rowData(se)$bla %in% c("LRG_239", "LRG_405"), "BLAAA", rowData(se)$bla )
res = aggregate_duplicates(se, .transcript = bla )
expect_equal(
as.data.frame(rowRanges(se["ENSG00000272397","SRR1039508"])) |>
mutate_if(is.factor, as.character),
as.data.frame(rowRanges(res["ENSG00000272397","SRR1039508"]))|>
mutate_if(is.factor, as.character),
)
expect_equal( dim(res), c( 99, 8 ) )
})
test_that("Add cell type proportions - SummarizedExperiment",{
res = deconvolve_cellularity(se_mini, cores=1 )
expect_equal(
as.numeric(as.data.frame(res@colData[1, 6:9])),
c( 0.619662 , 0.25256 , 0 , 0),
tolerance=1e-3
)
})
test_that("differential trancript abundance - SummarizedExperiment",{
res = test_differential_abundance(
se_mini |>
identify_abundant(factor_of_interest = condition),
~ condition
)
w = match( c("CLEC7A" , "FAM198B", "FCN1" , "HK3" ), rownames(res) )
# Quasi likelihood
res_tibble = test_differential_abundance(
input_df |> identify_abundant(a, b, c, factor_of_interest = condition),
~ condition ,
a, b, c
)
expect_equal(
res@elementMetadata[w,]$logFC,
c(-11.58385, -13.53406, -12.58204, -12.19271),
tolerance=1e-3
)
expect_equal(
res@elementMetadata[w,]$logFC,
res_tibble |>
pivot_transcript(b) |>
filter(b %in% rownames(res)[w]) |>
dplyr::arrange(b) |>
dplyr::pull(logFC),
tolerance=1e-3
)
# Likelihood ratio
res2 = test_differential_abundance(
se_mini |>
identify_abundant(factor_of_interest = condition),
~ condition, method = "edgeR_likelihood_ratio" )
res2_tibble = test_differential_abundance(
input_df |> identify_abundant(a, b, c, factor_of_interest = condition),
~ condition ,
a, b, c, method = "edgeR_likelihood_ratio"
)
expect_equal(
res2@elementMetadata[w,]$logFC,
c(-11.57989, -13.53476, -12.57969, -12.19303),
tolerance=1e-3
)
expect_equal(
res2@elementMetadata[w,]$logFC,
res2_tibble |>
pivot_transcript(b) |>
filter(b %in% rownames(res)[w]) |>
dplyr::arrange(b) |>
dplyr::pull(logFC),
tolerance=1e-3
)
# Treat
se_mini |>
identify_abundant(factor_of_interest = condition) |>
test_differential_abundance(
~ condition,
scaling_method = "TMM",
method = "edgeR_likelihood_ratio",
test_above_log2_fold_change = 1,
action="only"
) |> SummarizedExperiment::rowData() |>
as_tibble() |>
filter(FDR<0.05) |>
nrow() |>
expect_equal(171)
})
test_that("differential trancript abundance - SummarizedExperiment - alternative .abundance",{
library(SummarizedExperiment)
assays(se_mini) = list(counts = assay(se_mini), bla = assay(se_mini))
res = se_mini |>
identify_abundant(factor_of_interest = condition) |>
test_differential_abundance( ~ condition , .abundance = bla)
w = match( c("CLEC7A" , "FAM198B", "FCN1" , "HK3" ), rownames(res) )
# Quasi likelihood
res_tibble = test_differential_abundance(
input_df |> identify_abundant(a, b, c, factor_of_interest = condition),
~ condition ,
a, b, c
)
expect_equal(
res@elementMetadata[w,]$logFC,
c(-11.58385, -13.53406, -12.58204, -12.19271),
tolerance=1e-3
)
expect_equal(
res@elementMetadata[w,]$logFC,
res_tibble |>
pivot_transcript(b) |>
filter(b %in% rownames(res)[w]) |>
dplyr::arrange(b) |>
dplyr::pull(logFC),
tolerance=1e-3
)
# Likelihood ratio
res2 = test_differential_abundance(
se_mini |>
identify_abundant(factor_of_interest = condition),
~ condition, .abundance = bla, method = "edgeR_likelihood_ratio" )
res2_tibble = test_differential_abundance(
input_df |> identify_abundant(a, b, c, factor_of_interest = condition),
~ condition ,
a, b, c, method = "edgeR_likelihood_ratio"
)
expect_equal(
res2@elementMetadata[w,]$logFC,
c(-11.57989, -13.53476, -12.57969, -12.19303),
tolerance=1e-3
)
expect_equal(
res2@elementMetadata[w,]$logFC,
res2_tibble |>
pivot_transcript(b) |>
filter(b %in% rownames(res)[w]) |>
dplyr::arrange(b) |>
dplyr::pull(logFC),
tolerance=1e-3
)
# Treat
se_mini |>
identify_abundant( factor_of_interest = condition) |>
test_differential_abundance(
~ condition, .abundance = bla,
scaling_method = "TMM",
method = "edgeR_likelihood_ratio",
test_above_log2_fold_change = 1,
action="only"
) |> SummarizedExperiment::rowData() |>
as_tibble() |>
filter(FDR<0.05) |>
nrow() |>
expect_equal(171)
})
test_that("DE interaction effects", {
# Att interaction factor
col_data = colData(breast_tcga_mini_SE)
set.seed(42)
col_data$interaction_term = sample(c(0,1), size = nrow(col_data), replace = TRUE)
colData(breast_tcga_mini_SE) = col_data
breast_tcga_mini_SE |>
identify_abundant(factor_of_interest = Call) |>
test_differential_abundance(
~ Call * interaction_term,
contrasts = "CallHer2___interaction_term",
method="edgeR_quasi_likelihood"
) |>
expect_no_error()
})
test_that("Voom with treat method",{
se_mini |>
identify_abundant(factor_of_interest = condition) |>
test_differential_abundance(
~ condition,
method = "limma_voom",
test_above_log2_fold_change = 1,
action="only"
) |> SummarizedExperiment::rowData() |>
as_tibble() |>
filter(adj.P.Val<0.05) |>
nrow() |>
expect_equal(97)
# with multiple contrasts
res <-
se_mini |>
identify_abundant( factor_of_interest = Cell.type) |>
test_differential_abundance(
~ 0 + Cell.type,
.contrasts = c("Cell.typeb_cell-Cell.typemonocyte", "Cell.typeb_cell-Cell.typet_cell"),
method = "limma_voom",
test_above_log2_fold_change = 1,
action="only"
) |> SummarizedExperiment::rowData() |>
as_tibble()
res |>
filter(adj.P.Val___Cell.typeb_cell.Cell.typemonocyte < 0.05) |>
nrow() |>
expect_equal(294)
res |>
filter(adj.P.Val___Cell.typeb_cell.Cell.typet_cell < 0.05) |>
nrow() |>
expect_equal(246)
})
test_that("differential trancript abundance - random effects SE",{
set.seed(42)
res =
se_mini[1:10,] |>
identify_abundant(factor_of_interest = condition) |>
#mutate(time = time |> stringr::str_replace_all(" ", "_")) |>
test_differential_abundance(
~ condition + (1 + condition | time),
method = "glmmseq_lme4",
cores = 1
)
rowData(res)[,"P_condition_adjusted"] |>
head(4) |>
expect_equal(
c(0.1578695, 0.1221392, 0.1221392, 0.2262688),
tolerance=1e-2
)
# Custom dispersion
se_mini =
se_mini |>
identify_abundant(factor_of_interest = condition)
rowData(se_mini)$disp_ = rep(2,nrow(se_mini))
res =
se_mini[1:10,] |>
#mutate(time = time |> stringr::str_replace_all(" ", "_")) |>
test_differential_abundance(
~ condition + (1 + condition | time),
method = "glmmseq_lme4",
.dispersion = disp_,
cores = 1
)
rowData(res)[,"P_condition_adjusted"] |>
head(4) |>
expect_equal(
c(0.2633982, 0.2633982, 0.2633982, 0.5028348),
tolerance=1e-2
)
})
test_that("filter abundant - SummarizedExperiment",{
res = keep_abundant( se )
expect_equal( nrow(res), 23 )
})
test_that("filter variable - no object",{
res = keep_variable(se, top = 5 )
expect_equal( nrow(res),5 )
res =
keep_variable(
se_mini,
top = 5
)
expect_equal( nrow(res),5 )
expect_equivalent(
sort(rownames(res)),
c("FCN1", "IGHD", "IGHM", "IGKC", "TCL1A")
)
})
test_that("impute missing",{
res =
input_df |>
dplyr::slice(-1) |>
tidybulk:::tidybulk_to_SummarizedExperiment(a, b, c) |>
impute_missing_abundance( ~ condition )
list_SE = SummarizedExperiment::assays(res) |> as.list()
list_SE[[1]]["TNFRSF4", "SRR1740034"] |>
expect_equal(6)
expect_equal( nrow(res)*ncol(res), nrow(input_df) )
})
test_that("differential composition",{
# Cibersort
se_mini |>
test_differential_cellularity(. ~ condition , cores = 1 ) |>
pull(`estimate_(Intercept)`) |>
magrittr::extract2(1) |>
as.integer() |>
expect_equal( -2, tollerance =1e-3)
# llsr
se_mini |>
test_differential_cellularity(
. ~ condition,
method="llsr"
) |>
pull(`estimate_(Intercept)`) |>
magrittr::extract2(1) |>
as.integer() |>
expect_equal( -2, tollerance =1e-3)
# Survival analyses
input_df |>
dplyr::select(a, b, c) |>
nest(data = -a) |>
mutate(
days = c(1, 10, 500, 1000, 2000),
dead = c(1, 1, 1, 0, 1)
) |>
unnest(data) |>
tidybulk:::tidybulk_to_SummarizedExperiment(a, b, c) |>
test_differential_cellularity(
survival::Surv(days, dead) ~ .,
cores = 1
) |>
pull(estimate) |>
magrittr::extract2(1) |>
expect_equal(26.2662279, tolerance = 30)
# round() %in% c(
# 26, # 97 is the github action MacOS that has different value
# 26, # 112 is the github action UBUNTU that has different value
# 26 # 93 is the github action Windows that has different value
# ) |>
# expect_true()
})
test_that("test_stratification_cellularity",{
# Cibersort
input_df |>
select(a, b, c) |>
nest(data = -a) |>
mutate(
days = c(1, 10, 500, 1000, 2000),
dead = c(1, 1, 1, 0, 1)
) |>
unnest(data) |>
tidybulk:::tidybulk_to_SummarizedExperiment(a, b, c) |>
test_stratification_cellularity(
survival::Surv(days, dead) ~ .,
cores = 1
) |>
pull(.low_cellularity_expected) |>
magrittr::extract2(1) |>
expect_equal(3.35, tolerance =1e-1)
# llsr
input_df |>
select(a, b, c) |>
nest(data = -a) |>
mutate(
days = c(1, 10, 500, 1000, 2000),
dead = c(1, 1, 1, 0, 1)
) |>
unnest(data) |>
test_stratification_cellularity(
survival::Surv(days, dead) ~ .,
.sample = a,
.transcript = b,
.abundance = c,
method = "llsr"
) |>
pull(.low_cellularity_expected) |>
magrittr::extract2(1) |>
expect_equal(3.35, tolerance =1e-1)
})
# test_that("Get gene enrichment - no object",{
#
# if (find.package("EGSEA", quiet = TRUE) |> length |> equals(0)) {
# message("Installing EGSEA needed for differential transcript abundance analyses")
# if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager", repos = "https://cloud.r-project.org")
# BiocManager::install("EGSEA")
# }
#
# library(EGSEA)
#
# res =
# aggregate_duplicates(
# dplyr::rename(symbol_to_entrez(
# #dplyr::filter(input_df, grepl("^B", b)),
# input_df,
# .transcript = b, .sample = a), d = entrez
# ),
# .transcript = d,
# .sample = a,
# .abundance = c
# ) |> identify_abundant(a, b, c, factor_of_interest = condition) |>
# tidybulk:::tidybulk_to_SummarizedExperiment(a, b, c) |>
# test_gene_enrichment(
# ~ condition,
# .entrez = d,
# species="human"
# )
#
# expect_equal(
# res$pathway[1:4],
# c("GNF2_HCK" , "GSE10325_LUPUS_BCELL_VS_LUPUS_MYELOID_DN" ,"Amino sugar and nucleotide sugar metabolism", "Phagosome" )
# )
#
# expect_equal(
# ncol(res),
# 20
# )
#
# })
test_that("pivot",{
expect_equal( ncol(pivot_sample(se_mini) ), 6)
expect_equal( ncol(pivot_transcript(se_mini) ), 2)
})
test_that("gene over representation",{
df_entrez = aggregate_duplicates(input_df, aggregation_function = sum, .sample = a, .transcript = entrez, .abundance = c)
df_entrez = mutate(df_entrez, do_test = b %in% c("TNFRSF4", "PLCH2", "PADI4", "PAX7"))
res =
df_entrez |>
tidybulk:::tidybulk_to_SummarizedExperiment(a, b, c) |>
test_gene_overrepresentation(
.entrez = entrez,
.do_test = do_test,
species="Homo sapiens"
)
expect_equal( ncol(res), 13 )
})
test_that("Only reduced dimensions MDS - no object",{
res =
breast_tcga_mini_SE |>
reduce_dimensions(method = "MDS")
expect_equal(
res$`Dim1`[1:4],
c(-0.2723808836, -0.1105770207, -0.3034092668, -0.0064569358),
tolerance=10
)
expect_equal(
ncol(SummarizedExperiment::colData(res)),
3
)
expect_equal( class(attr(res, "internals")$MDS[[1]])[1], "MDS" )
})
test_that("Only reduced dimensions PCA - no object",{
res =
breast_tcga_mini_SE |>
reduce_dimensions( method = "PCA" )
expect_equal(
res$`PC1`[1:4],
c(-8.5145575 , 4.2451190 , -6.8991306 , -6.0787597 ),
tolerance=10
)
expect_equal(
ncol(SummarizedExperiment::colData(res)),
3
)
expect_equal( class(attr(res, "internals")$PCA[[1]])[1], "numeric" )
})
test_that("Only reduced dimensions tSNE - no object",{
res =
breast_tcga_mini_SE |>
reduce_dimensions( method = "tSNE" )
expect_equal(
res$`tSNE1`[1:4],
c(-2.4677708, -0.3447403, -5.8059667, 1.9685007 ),
tolerance=10
)
expect_equal(
ncol(SummarizedExperiment::colData(res)),
3
)
expect_equal( class(attr(res, "internals")$tSNE[[1]])[1], "integer" )
})
test_that("Only reduced dimensions UMAP - no object",{
res =
breast_tcga_mini_SE |>
reduce_dimensions( method = "UMAP" )
expect_equal(
res$`UMAP1`[1:4],
c(-1.9784263, -0.8536380, -0.6537955, -1.8840860 ),
tolerance=10
)
expect_equal(
ncol(SummarizedExperiment::colData(res)),
3
)
expect_equal( class(attr(res, "internals")$UMAP[[1]])[1], "numeric" )
})
test_that("resolve_complete_confounders_of_non_interest",{
#library(tidySummarizedExperiment)
library(SummarizedExperiment)
# Sample annotations
sample_annotations <- data.frame(
sample_id = paste0("Sample", seq(1, 9)),
factor_of_interest = c(rep("treated", 4), rep("untreated", 5)),
A = c("a1", "a2", "a1", "a2", "a1", "a2", "a1", "a2", "a3"),
B = c("b1", "b1", "b2", "b1", "b1", "b1", "b2", "b1", "b3"),
C = c("c1", "c1", "c1", "c1", "c1", "c1", "c1", "c1", "c3"),
stringsAsFactors = FALSE
)
# Simulated assay data (e.g., gene expression data)
# Let's assume we have 100 genes (rows) and 9 samples (columns)
assay_data <- matrix(rnorm(100 * 9), nrow = 100, ncol = 9)
# Row data (e.g., gene annotations)
# For simplicity, we'll just use a sequence of gene IDs
row_data <- data.frame(gene_id = paste0("Gene", seq_len(100)))
# Create SummarizedExperiment object
se <- SummarizedExperiment(assays = list(counts = assay_data),
rowData = row_data,
colData = DataFrame(sample_annotations))
expected_tibble =
tibble(
.sample = c("1", "5", "2", "4", "6", "8", "9", "3", "7"),
A = c("a1", "a1", "a2", "a2", "a2", "a2", "a3", "a1", "a1"),
B = c("b1", "b1", "b1", "b1", "b1", "b1", "b1", "b2", "b2"),
C = rep("c1", 9)
) |> arrange(.sample)
se |>
resolve_complete_confounders_of_non_interest(A, B, C) |>
colData() |>
_[, c("A", "B", "C")] |>
as_tibble(rownames = ".sample") |>
expect_identical(expected_tibble )
})
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