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Merged
PMSeitzer merged 3 commits into from
Mar 31, 2026
Merged

Support alternative mzroll list import #50

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7e44736
Issue 12: Styler formatting.
PMSeitzer Mar 26, 2026
a876400
Issue 12: Styler formatting.
PMSeitzer Mar 26, 2026
2d0bb18
Issue 12: Implemented type overloading on mzroll_db_path to support p…
PMSeitzer Mar 26, 2026
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14 changes: 13 additions & 1 deletion R/import_mzroll.R
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Original file line number Diff line number Diff line change
@@ -1,6 +1,10 @@
#' Process mzRoll
#'
#' @param mzroll_db_path path to mzroll DB file
#' @param mzroll_db_path path to mzroll DB file,
#' or a pre-built romic triple_omic object with type tag 'mzroll'.
#' Callers of this function are responsible for passing in a valid input object
#' in that use case. However, the object will still be tested via
#' \code{test_mzroll_list()}.
#' @param only_identified TRUE/FALSE, filter to only features which were
#' identified.
#' @param validate TRUE/FALSE, use meta-data to only name the subset of
Expand Down Expand Up @@ -37,6 +41,14 @@ process_mzroll <- function(mzroll_db_path,
peakgroup_labels_to_keep = "*",
peakgroup_labels_to_exclude = "",
quant_col = "peakAreaTop") {
# Issue 12: Support import of pre-built 'mzroll' tomic (romic tiple omic) object.
# Callers are responsible to generate a valid 'mzroll' object.
# test_mzroll_list() will fail if object is invalid.
if ("mzroll" %in% class(mzroll_db_path)) {
test_mzroll_list(mzroll_db_path)
return(mzroll_db_path)
}

checkmate::assertFileExists(mzroll_db_path)
checkmate::assertLogical(only_identified, len = 1)
checkmate::assertLogical(validate, len = 1)
Expand Down
6 changes: 5 additions & 1 deletion man/process_mzroll.Rd
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11 changes: 5 additions & 6 deletions tests/testthat/test_mutates.R
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Original file line number Diff line number Diff line change
Expand Up @@ -82,32 +82,31 @@ test_that("Test reference samples and reference conditions", {
})

test_that("Flooring adds missing peaks", {

# discard random measurements representing peaks that weren't
# picked due to being below the limit of detection

nplug_with_missing_values <- nplug_mzroll_augmented
nplug_with_missing_values$measurements <- nplug_mzroll_augmented$measurements %>%
dplyr::anti_join(
nplug_mzroll_augmented$measurements %>%
dplyr::sample_n(100),
by = c("groupId", "sampleId")
)

floored_nplug <- floor_peaks(nplug_with_missing_values)

peakgroups_with_missing_vals <- floored_nplug$measurements %>%
dplyr::count(groupId) %>%
dplyr::filter(n != max(n))

expect_equal(nrow(peakgroups_with_missing_vals), 0)
})

test_that("Flooring works and is maintained", {
floored_peaks <- claman::floor_peaks(
nplug_mzroll_augmented,
log2_floor_value = 12
)
)

expect_equal(
floored_peaks$measurements$log2_abundance >= 12,
Expand Down
65 changes: 33 additions & 32 deletions vignettes/NPLUG.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ mzroll_list_augmented <- merge_samples_tbl(
nplug_samples,
"sample_name",
exact = TRUE
)
)
```

```{r read_sample_metadata_tables, echo = FALSE}
Expand Down Expand Up @@ -105,7 +105,7 @@ romic::plot_heatmap(
sample_var = "name",
value_var = "centered_log2_abundance",
change_threshold = 5
) + facet_grid(~ exp_ref + limitation, scales = "free_x", space = "free_x") +
) + facet_grid(~ exp_ref + limitation, scales = "free_x", space = "free_x") +
ggtitle("Metabolites separated by limiting nutrients")
```

Expand All @@ -124,7 +124,7 @@ romic::plot_heatmap(
sample_var = "name",
value_var = "centered_log2_abundance",
change_threshold = 5
) + facet_grid(~ limitation + extraction, scales = "free_x", space = "free_x") +
) + facet_grid(~ limitation + extraction, scales = "free_x", space = "free_x") +
ggtitle("Metabolites separated by extraction") +
theme(strip.text = element_text(size = 10))
```
Expand All @@ -141,12 +141,12 @@ mzroll_list_augmented %>%
filter_table = "samples",
filter_variable = "exp_ref",
filter_value = "ref"
) %>%
) %>%
romic::plot_heatmap(
feature_var = "compoundName",
sample_var = "name",
value_var = "centered_log2_abundance",
change_threshold = 5
feature_var = "compoundName",
sample_var = "name",
value_var = "centered_log2_abundance",
change_threshold = 5
) + facet_grid(~ month + DR, scales = "free_x", space = "free_x") +
ggtitle("References separated by month and distinct cultures (by DR)") +
theme(strip.text = element_text(size = 10))
Expand All @@ -171,14 +171,14 @@ plot_compare_injection(
mzroll_list_augmented,
grouping_vars = "condition",
peak_quant_var = "centered_log2_abundance"
) + ggtitle("Comparison of injection technical replicates")
) + ggtitle("Comparison of injection technical replicates")

mzroll_list_distinct_conditions <- collapse_injections(
mzroll_list_augmented,
grouping_vars = "condition",
peak_quant_vars = c("log2_abundance", "centered_log2_abundance"),
collapse_fxn = "mean"
)
)
```

```{r technical_replicates_table, echo = FALSE}
Expand All @@ -201,7 +201,7 @@ mzroll_list_normalized <- normalize_peaks(
batch_varnames = c("month", "extraction"),
reference_varname = "exp_ref",
reference_values = "ref"
) %>%
) %>%
# having normalized by the common reference, we can re-center the data
# since slow-phosphate limited growth is not a biological reference.
romic::center_tomic(measurement_vars = "normalized_log2_abundance")
Expand All @@ -217,7 +217,7 @@ romic::plot_heatmap(
value_var = "normalized_log2_abundance",
change_threshold = 5,
cluster_dim = "rows"
) + facet_grid(~ exp_ref + limitation, scales = "free_x", space = "free_x") +
) + facet_grid(~ exp_ref + limitation, scales = "free_x", space = "free_x") +
ggtitle("Post-normalization metabolite abundances") +
theme(strip.text = element_text(size = 10))
```
Expand All @@ -236,15 +236,15 @@ final_processed_data <- mzroll_list_normalized %>%
filter_table = "samples",
filter_variable = "exp_ref",
filter_value = "exp"
) %>%
) %>%
# retain only filter extraction
romic::filter_tomic(
filter_type = "category",
filter_table = "samples",
filter_variable = "extraction",
filter_value = "filter"
)
)

# clean-up sample data
renamed_samples <- final_processed_data$samples %>%
select(sampleId, limitation, DR) %>%
Expand All @@ -254,14 +254,14 @@ renamed_samples <- final_processed_data$samples %>%
group_by(name) %>%
mutate(name = case_when(
n() == 1 ~ name,
TRUE ~ paste0(name, "-", 1:n()))
) %>%
TRUE ~ paste0(name, "-", 1:n())
)) %>%
ungroup()

final_processed_data <- romic::update_tomic(
final_processed_data,
renamed_samples
)
)

romic::plot_heatmap(
final_processed_data,
Expand All @@ -270,7 +270,7 @@ romic::plot_heatmap(
value_var = "normalized_log2_abundance",
change_threshold = 5,
cluster_dim = "rows"
) + facet_grid(~ limitation, scales = "free_x", space = "free_x") +
) + facet_grid(~limitation, scales = "free_x", space = "free_x") +
ggtitle("Final processed metabolite abundances across 25 growth conditions") +
theme(strip.text = element_text(size = 10))
```
Expand All @@ -294,7 +294,7 @@ romic::plot_bivariate(
"PC1",
"PC2",
color_var = "limitation"
) + ggtitle("Top principal components driving metabolomic variation")
) + ggtitle("Top principal components driving metabolomic variation")
```

One plot doesn't quite cut it here. Luckily, romic has some powerful methods for shiny-based interactive analysis that we can leverage here to quickly make plots like these.
Expand All @@ -320,7 +320,7 @@ regression_significance <- diffex_mzroll(
final_processed_data,
"normalized_log2_abundance",
"limitation + limitation:DR + 0"
)
)

plot_pvalues(regression_significance)
plot_volcano(regression_significance)
Expand All @@ -335,7 +335,8 @@ n_lim_signif <- regression_significance %>%
left_join(
final_processed_data$features %>%
select(groupId, peak_label),
by = "groupId")
by = "groupId"
)
```

```{r met_examples_table, echo = FALSE}
Expand All @@ -352,7 +353,7 @@ plot_barplot(
grouping_vars = c("limitation", "DR"),
value_var = "normalized_log2_abundance",
fill_var = "limitation"
) + scale_fill_brewer(palette = "Set2")
) + scale_fill_brewer(palette = "Set2")
```

## Pathway Analysis
Expand All @@ -364,18 +365,18 @@ pathway_nest <- final_processed_data$features %>%

pathway_list <- purrr::map(
pathway_nest$pathway_members,
function(x) {
as.character(x$groupId)
}
)
function(x) {
as.character(x$groupId)
}
)
names(pathway_list) <- pathway_nest$pathway

enrichments <- find_pathway_enrichments(
final_processed_data,
regression_significance,
pathway_list,
test_absolute_effects = FALSE
)
)
```

### Generate tables and plots of top enrichments
Expand All @@ -397,7 +398,7 @@ ranked_nitrogen_enrichments$enrichment_plot[[1]] +
ggtitle(
"Amino acids are depleted during nitrogen limitation",
"Note that the x-axis is ranks, and negative values have higher ranks"
)
)
```

# Export results
Expand All @@ -420,13 +421,13 @@ final_processed_data <- romic::update_tomic(
util_pretty_khead(
final_processed_data$features,
caption = "Peakgroups with differential abundance statistics added"
)
)
```

```{r export_results, eval = FALSE}
romic::export_tomic_as_tidy(
final_processed_data,
dir_path = "/tmp",
name_preamble = "nplug"
)
)
```
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